Rv3545c

Tuberculist information
Gene namecyp125
Protein functionProbable cytochrome P450 125 Cyp125
Functional category(tuberculist)intermediary metabolism and respiration
Gene location(kb)3984.14
Molecular mass(da)48400.6
External sites TB Database TubercuList WebTB
Protein sequence
Number of amino acids : 433
	  		  	1    VSWNHQSVEIAVRRTTVPSPNLPPGFDFTDPAIYAERLPVAEFAELRSAAPIWWNGQDPG   60
			  	61   KGGGFHDGGFWAITKLNDVKEISRHSDVFSSYENGVIPRFKNDIAREDIEVQRFVMLNMD  120
			  	121  APHHTRLRKIISRGFTPRAVGRLHDELQERAQKIAAEAAAAGSGDFVEQVSCELPLQAIA  180
			  	181  GLLGVPQEDRGKLFHWSNEMTGNEDPEYAHIDPKASSAELIGYAMKMAEEKAKNPADDIV  240
			  	241  TQLIQADIDGEKLSDDEFGFFVVMLAVAGNETTRNSITQGMMAFAEHPDQWELYKKVRPE  300
			  	301  TAADEIVRWATPVTAFQRTALRDYELSGVQIKKGQRVVMFYRSANFDEEVFQDPFTFNIL  360
			  	361  RNPNPHVGFGGTGAHYCIGANLARMTINLIFNAVADHMPDLKPISAPERLRSGWLNGIKH  420
			  	421  WQVDYTGRCPVAH

Known structures in the PDB
PDB ID2X5L
Total residue count431
Number of chains1
MethodX-RAY
Resolution1.48
PDB ID2X5W
Total residue count440
Number of chains1
MethodX-RAY
Resolution1.58
PDB ID2XC3
Total residue count424
Number of chains1
MethodX-RAY
Resolution1.5
PDB ID2XN8
Total residue count423
Number of chains1
MethodX-RAY
Resolution1.64
PDB ID3IVY
Total residue count433
Number of chains1
MethodX-RAY
Resolution1.35
PDB ID3IW0
Total residue count433
Number of chains1
MethodX-RAY
Resolution1.7
PDB ID3IW1
Total residue count433
Number of chains1
MethodX-RAY
Resolution2
PDB ID3IW2
Total residue count433
Number of chains1
MethodX-RAY
Resolution2.19
1 44 87 130 173 216 259 302 345 388 431 Range: 300 to 397  |  Coverage: 22% p450 Range: 20 to 427  |  Coverage: 93% 1 Range: 40 to 427  |  Coverage: 89% 2 Range: 7 to 429  |  Coverage: 97% 3 Range: 1 to 95  |  Coverage: 21% 1 Range: 209 to 303  |  Coverage: 21% 2 Range: 300 to 394  |  Coverage: 21% 3
Number of amino acids : 433
Domains assigned based on sequence. Mtb Structural proteome models CHOPIN models
Profile-based domain assignment
Structural/Functional domain familyPfam acc.no./SCOP IDDomain Region
p450PF00067300-397
Mtb Structural Proteome models
Model Number1
Model nameRv3545c_3ivy_A
Template3IVY    APDBCREDO
Template coverage20_427
Template Identity(%)100.0
Model coverage(%)94.0
Normalized DOPE score-2.012

Model Number2
Model nameRv3545c
Template1CPT    APDBCREDO
Template coverage28_427
Template Identity(%)28.6
Model coverage(%)89.4
Normalized DOPE score-0.846

Model Number3
Model nameRv3545c.1
Template1TQN    APDBCREDO
Template coverage29_497
Template Identity(%)16.1
Model coverage(%)97.5
Normalized DOPE score-0.072

Structure Models from Chopin
Model Number1
Profilea.104.1.1 - 1.10.630.10
Click for model details
zscore5.22
Residue begin1
Residue end95
Model Number2
Profilea.104.1.1 - 1.10.630.10
Click for model details
zscore5.22
Residue begin209
Residue end303
Model Number3
Profilea.104.1.1 - 1.10.630.10
Click for model details
zscore5.22
Residue begin300
Residue end394
Binding pockets
STRING
Cytoscape Web will replace the contents of this div with protein-protein interaction network.
Protein interacting with Rv3545cGene nameConfidence Score
Rv3540cltp20.975
Rv3540cltp20.975
Rv2276cyp1210.96
Rv3541cRv3541c0.948
Rv1777cyp1440.947
Rv1256ccyp1300.946
Rv2268ccyp1280.945
Rv0892Rv08920.938
Rv3121cyp1410.936
Rv3518ccyp1420.934
Rv1785ccyp1430.929
Rv1880ccyp1400.926
Rv3685ccyp1370.925
Rv3542cRv3542c0.924
Rv3542cRv3542c0.924
Rv0136cyp1380.922
Rv0766ccyp1230.919
Rv2266cyp1240.919
Rv3544cfadE280.916
Rv3544cfadE280.916
Rv1394ccyp1320.913
Rv3059cyp1360.913
Rv0778cyp1260.912
Rv0568cyp135B10.909
Rv0327ccyp135A10.908
Rv3543cfadE290.908
Rv3543cfadE290.908
Rv3543cfadE290.908
Potential ligand/drug binding sites
No binding sites identified
Similarity to known drug target from sensitive sequence analysis
No drug targets
List of small molecules tested from TIBLE
  View results in TIBLE page
NameAffinityAssay descriptionDOI
CHEMBL112570ActiveBinding affinity to Mycobacterium tuberculosis CYP125A1 assessed as type 1 binding mode at 0.05 to 0.2 uM by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL112570Kcat(app) = 28 /minActivity of Mycobacterium tuberculosis CYP125A1 assessed as apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL194859Not ActiveBinding affinity to Mycobacterium tuberculosis His4-tagged recombinant CYP125 expressed in Escherichia coli HMS174(DE3) by UV-visible spectral titration methodhttp://www.ncbi.nlm.nih.gov/pubmed/17846131
CHEMBL2048316Kcat(app) = 5.1 /minActivity of Mycobacterium tuberculosis CYP125A1 assessed as apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048316Activity = 18 %Activity of Mycobacterium tuberculosis CYP125A1 assessed as relative apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS method relative to cholesterolhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048316ActiveBinding affinity to Mycobacterium tuberculosis CYP125A1 assessed as type 1 binding mode at 0.05 to 0.2 uM by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048317ActiveBinding affinity to Mycobacterium tuberculosis CYP125A1 assessed as type 1a binding mode at > 0.05 to 0.2 uM by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048318Activity = 37 %Activity of Mycobacterium tuberculosis CYP125A1 assessed as relative apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS method relative to cholesterolhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048318Kcat(app) = 10.7 /minActivity of Mycobacterium tuberculosis CYP125A1 assessed as apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048318ActiveBinding affinity to Mycobacterium tuberculosis CYP125A1 assessed as type 1a binding mode at > 0.05 to 0.2 uM by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048318Kd(app) = 0.25 uMBinding affinity to Mycobacterium tuberculosis CYP125A1 by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048319Kd(app) = 0.45 uMBinding affinity to Mycobacterium tuberculosis CYP125A1 by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048319Kcat(app) = 8.1 /minActivity of Mycobacterium tuberculosis CYP125A1 assessed as apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048319Activity = 29.9 %Activity of Mycobacterium tuberculosis CYP125A1 assessed as relative apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS method relative to cholesterolhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048319ActiveBinding affinity to Mycobacterium tuberculosis CYP125A1 assessed as type 1 binding mode at 0.05 to 0.2 uM by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048320Activity = 68.1 %Activity of Mycobacterium tuberculosis CYP125A1 assessed as relative apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS method relative to cholesterolhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048320ActiveBinding affinity to Mycobacterium tuberculosis CYP125A1 assessed as type 1 binding mode at 0.05 to 0.2 uM by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048320Kcat(app) = 19 /minActivity of Mycobacterium tuberculosis CYP125A1 assessed as apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048321ActiveBinding affinity to Mycobacterium tuberculosis CYP125A1 assessed as type 1 binding mode at 0.05 to 0.2 uM by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048321Not ActiveTime dependent inhibition of Mycobacterium tuberculosis CYP125A1 at 50 uM incubated up to 3 hrs by HPLChttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048321Kcat(app) = 2.2 /minActivity of Mycobacterium tuberculosis CYP125A1 assessed as apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048321Activity = 8 %Activity of Mycobacterium tuberculosis CYP125A1 assessed as relative apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS method relative to cholesterolhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048322Activity = 26 %Activity of Mycobacterium tuberculosis CYP125A1 assessed as relative apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS method relative to cholesterolhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048322ActiveBinding affinity to Mycobacterium tuberculosis CYP125A1 assessed as type 1 binding mode at 0.05 to 0.2 uM by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048322Kcat(app) = 7.29 /minActivity of Mycobacterium tuberculosis CYP125A1 assessed as apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048323Kcat(app) = 18.22 /minActivity of Mycobacterium tuberculosis CYP125A1 assessed as apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048323ActiveBinding affinity to Mycobacterium tuberculosis CYP125A1 assessed as type 1 binding mode at 0.05 to 0.2 uM by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048323Activity = 65.1 %Activity of Mycobacterium tuberculosis CYP125A1 assessed as relative apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS method relative to cholesterolhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048324ActiveBinding affinity to Mycobacterium tuberculosis CYP125A1 assessed as type 1a binding mode at > 0.05 to 0.2 uM by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048325Kcat(app) = 14.24 /minActivity of Mycobacterium tuberculosis CYP125A1 assessed as apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048325Activity = 50.9 %Activity of Mycobacterium tuberculosis CYP125A1 assessed as relative apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS method relative to cholesterolhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048325ActiveBinding affinity to Mycobacterium tuberculosis CYP125A1 assessed as type 1 binding mode at 0.05 to 0.2 uM by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048326ActiveActivity of Mycobacterium tuberculosis CYP125A1 assessed as compound oxidation at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048327ActiveActivity of Mycobacterium tuberculosis CYP125A1 assessed as compound oxidation at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048328ActiveActivity of Mycobacterium tuberculosis CYP125A1 assessed as compound oxidation at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048329ActiveActivity of Mycobacterium tuberculosis CYP125A1 assessed as compound oxidation at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048330ActiveActivity of Mycobacterium tuberculosis CYP125A1 assessed as compound oxidation at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048331ActiveActivity of Mycobacterium tuberculosis CYP125A1 assessed as compound oxidation at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048332ActiveActivity of Mycobacterium tuberculosis CYP125A1 assessed as compound oxidation at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048333ActiveActivity of Mycobacterium tuberculosis CYP125A1 assessed as compound oxidation at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048334ActiveActivity of Mycobacterium tuberculosis CYP125A1 assessed as compound oxidation at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048335ActiveActivity of Mycobacterium tuberculosis CYP125A1 assessed as compound oxidation at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL2048336ActiveActivity of Mycobacterium tuberculosis CYP125A1 assessed as compound oxidation at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL225111ActiveBinding affinity to Mycobacterium tuberculosis CYP125A1 assessed as type 1 binding mode at 0.05 to 0.2 uM by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL225111Kcat(app) = 10.37 /minActivity of Mycobacterium tuberculosis CYP125A1 assessed as apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL225111Activity = 37 %Activity of Mycobacterium tuberculosis CYP125A1 assessed as relative apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS method relative to cholesterolhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL455876Activity = 47.5 %Activity of Mycobacterium tuberculosis CYP125A1 assessed as relative apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS method relative to cholesterolhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL455876Kcat(app) = 13.29 /minActivity of Mycobacterium tuberculosis CYP125A1 assessed as apparent turnover number at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL455876ActiveBinding affinity to Mycobacterium tuberculosis CYP125A1 assessed as type 1 binding mode at 0.05 to 0.2 uM by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL507264Kd = 2 mMBinding affinity to Mycobacterium tuberculosis His4-tagged recombinant CYP125 expressed in Escherichia coli HMS174(DE3) by UV-visible spectral titration methodhttp://www.ncbi.nlm.nih.gov/pubmed/17846131
CHEMBL63243ActiveActivity of Mycobacterium tuberculosis CYP125A1 assessed as compound oxidation at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL63243ActiveBinding affinity to Mycobacterium tuberculosis CYP125A1 assessed as type 1 binding mode at 0.05 to 0.2 uM by UV-visible spectrophotometryhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
CHEMBL69851ActiveActivity of Mycobacterium tuberculosis CYP125A1 assessed as compound oxidation at 50 uM incubated for 1 hr at 25 degC by GC-MS methodhttp://www.ncbi.nlm.nih.gov/pubmed/22647881
Off-target activity - ligand based from TIBLE
  View results in TIBLE page
Predicted off-targetMethodSummaryFull results
Cathepsin K 1TU6PharmMapper3 hydroph + 6 HB + 0 pos/neg + 0 aromLink
Stromelysin-1 1CIZPharmMapper5 hydroph + 3 HB + 1 pos/neg + 0 aromLink
Neprilysin 1R1HPharmMapper3 hydroph + 5 HB + 2 pos/neg + 0 aromLink
Angiotensin-converting enzyme 1UZFPharmMapper2 hydroph + 3 HB + 2 pos/neg + 0 aromLink
Aldose reductase 2DUXPharmMapper4 hydroph + 5 HB + 1 pos/neg + 2 aromLink
Acyl coenzyme A:cholesterol acyltransferase 1 SEAE_value = 7.89e-50 & MaxTC = 0.44Link
sphingosine 1-phosphate receptor 4; endothelial differentiation G-protein coupled receptor 6 SEAE_value = 8.67e-37 & MaxTC = 0.33Link
Histone deacetylase 2 SEAE_value = 9.59e-35 & MaxTC = 0.67Link
interleukin-4; B-cell stimulatory factor 1 [-] SEAE_value = 1.46e-34 & MaxTC = 0.38Link
Histone deacetylase 3 SEAE_value = 7.96e-32 & MaxTC = 0.67Link
Neurokinin 3 receptor SEAE_value = 8.03e-31 & MaxTC = 0.33Link
Histone deacetylase 9 SEAE_value = 4.8e-29 & MaxTC = 0.67Link
Histone deacetylase 5 SEAE_value = 5.01e-29 & MaxTC = 0.67Link
interleukin-5; T-cell replacing factor [-] SEAE_value = 1.53e-28 & MaxTC = 0.38Link
Neuropeptide Y Antagonist SEAE_value = 9.87e-28 & MaxTC = 0.57Link
Histone deacetylase 1 SEAE_value = 3.24e-26 & MaxTC = 0.67Link
sphingosine 1-phosphate receptor 5; endothelial differentiation sphingolipid G-protein-coupled receptor 8 SEAE_value = 1.11e-24 & MaxTC = 0.33Link
sphingosine 1-phosphate receptor 1 SEAE_value = 1.11e-24 & MaxTC = 0.33Link
sphingosine 1-phosphate receptor 3 SEAE_value = 1.11e-24 & MaxTC = 0.33Link
sphingosine 1-phosphate receptor 2; endothelial differentiation G-protein coupled receptor 5 SEAE_value = 1.11e-24 & MaxTC = 0.33Link
Beta-chymotrypsin SEAE_value = 1.74e-17 & MaxTC = 0.32Link
Matrix metalloproteinase 3 SEAE_value = 9.19e-16 & MaxTC = 0.42Link
histone deacetylase 1 [-] SEAE_value = 5.73e-15 & MaxTC = 0.67Link
Factor VIIa Inhibitor SEAE_value = 6.28e-15 & MaxTC = 0.39Link
Anandamide amidohydrolase SEAE_value = 9.86e-14 & MaxTC = 0.34Link
Dipeptidyl peptidase I SEAE_value = 1.28e-12 & MaxTC = 0.31Link
ACAT Inhibitor SEAE_value = 1.34e-12 & MaxTC = 0.44Link
carbonic anhydrase VA; mitochondrial [-] SEAE_value = 1.45e-12 & MaxTC = 0.36Link
Leukotriene A4 hydrolase SEAE_value = 5.92e-12 & MaxTC = 0.38Link
potassium-transporting ATPase [-] SEAE_value = 6.91e-12 & MaxTC = 0.42Link
Oligopeptide transporter small intestine isoform SEAE_value = 2.85e-11 & MaxTC = 0.29Link
histone deacetylase 1 [-] SEAE_value = 3.25e-11 & MaxTC = 0.33Link
Small molecules involved in protein-protein complex from TIMBAL .Proteins similar to Mtb based on sequence analysis.
Data not available
STITCH interactions  
Chemical NameConfidence scoreMolecular Weight
androstenedionePubChem0.983286.409
cholest-4-en-3-onePubChem0.961384.638
hydron sulfatePubChem0.905196.157
sulfatePubChem0.90596.0626
catecholPubChem0.9110.111
C16205PubChem0.9212.244
phosphatePubChem0.996.9872
EKOPubChem0.9381.684
myrtenolPubChem0.9152.233
polyethylene glycolPubChem0.962.0678
trans-pinocarveolPubChem0.9152.233
RT8PubChem0.9404.505
hydron diphosphatePubChem0.9391.981
monoterpenesPubChem0.9136.234
ethylene glycol; hydronPubChem0.963.0758
1,2,4-benzenetriolPubChem0.9126.11