Rv0467

Tuberculist information
Gene nameicl1
Protein functionIsocitrate lyase Icl (isocitrase) (isocitratase)
Functional category(tuberculist)intermediary metabolism and respiration
Gene location(kb)557.527
Molecular mass(da)47086.6
External sites TB Database TubercuList WebTB
Protein sequence
Number of amino acids : 428
	  		  	1    MSVVGTPKSAEQIQQEWDTNPRWKDVTRTYSAEDVVALQGSVVEEHTLARRGAEVLWEQL   60
			  	61   HDLEWVNALGALTGNMAVQQVRAGLKAIYLSGWQVAGDANLSGHTYPDQSLYPANSVPQV  120
			  	121  VRRINNALQRADQIAKIEGDTSVENWLAPIVADGEAGFGGALNVYELQKALIAAGVAGSH  180
			  	181  WEDQLASEKKCGHLGGKVLIPTQQHIRTLTSARLAADVADVPTVVIARTDAEAATLITSD  240
			  	241  VDERDQPFITGERTREGFYRTKNGIEPCIARAKAYAPFADLIWMETGTPDLEAARQFSEA  300
			  	301  VKAEYPDQMLAYNCSPSFNWKKHLDDATIAKFQKELAAMGFKFQFITLAGFHALNYSMFD  360
			  	361  LAYGYAQNQMSAYVELQEREFAAEERGYTATKHQREVGAGYFDRIATTVDPNSSTTALTG  420
			  	421  STEEGQFH

Known structures in the PDB
PDB ID1F61
Total residue count858
Number of chains2
MethodX-RAY
Resolution2
PDB ID1F8I
Total residue count1716
Number of chains4
MethodX-RAY
Resolution2.25
PDB ID1F8M
Total residue count1716
Number of chains4
MethodX-RAY
Resolution1.8
1 43 85 127 169 211 253 295 337 379 421 Range: 9 to 254  |  Coverage: 57% ICL Range: 1 to 427  |  Coverage: 99% 1 Range: 2 to 427  |  Coverage: 99% 2 Range: 63 to 354  |  Coverage: 67% 1
Number of amino acids : 428
Domains assigned based on sequence. Mtb Structural proteome models CHOPIN models
Profile-based domain assignment
Structural/Functional domain familyPfam acc.no./SCOP IDDomain Region
ICLPF004639-254
Mtb Structural Proteome models
Model Number1
Model nameRv0467_1f8m_A
Template1F8M    APDBCREDO
Template coverage1_427
Template Identity(%)100.0
Model coverage(%)99.5
Normalized DOPE score-1.141

Model Number2
Model nameRv0467
Template1F8M    APDBCREDO
Template coverage2_427
Template Identity(%)100.0
Model coverage(%)99.3
Normalized DOPE score-0.891

Structure Models from Chopin
Model Number1
Profilec.1.12.7 - 3.20.20.60
Click for model details
zscore28.14
Residue begin63
Residue end354
Binding pockets
STRING
Cytoscape Web will replace the contents of this div with protein-protein interaction network.
Protein interacting with Rv0467Gene nameConfidence Score
Rv1837cglcB0.997
Rv1475cacn0.977
Rv1475cacn0.977
Rv1131prpC0.945
Rv1240mdh0.945
Rv1240mdh0.945
Rv0468fadB20.941
Rv0468fadB20.941
Rv2967cpca0.931
Rv2967cpca0.931
Rv2967cpca0.931
Rv2967cpca0.931
Rv2967cpca0.931
Rv2967cpca0.931
Rv3667acs0.918
Rv1257cRv1257c0.918
Rv1257cRv1257c0.918
Rv3667acs0.918
Rv0409ackA0.917
Potential ligand/drug binding sites
Protein ModelPocket NumberDrug Binding Site PMIN ScorePvalue PMINPMAX ScorePvalue PMAX
Rv0467_1f8m_A361s9p_DES_C_500PDBCREDO0.5580.2330.5360.006
Rv0467_1f8m_A363qlg_1N1_B_601PDBCREDO0.5350.2660.5350.006
Rv0467_1f8m_A362zva_1N1_A_513PDBCREDO0.5550.2380.5330.007
Rv0467_1f8m_A362cbr_A80_A_201PDBCREDO0.5750.2110.5320.007
Rv0467_1f8m_A361s9p_DES_B_459PDBCREDO0.5540.2390.5320.007
Rv0467_1f8m_A363g5d_1N1_B_1PDBCREDO0.5290.2750.5290.007
Rv0467_1f8m_A361jzs_MRC_A_1301PDBCREDO0.5460.2500.5250.007
Rv0467_1f8m_A361kij_NOV_B_444PDBCREDO0.5450.2510.5250.007
Rv0467_1f8m_A363qlg_1N1_A_601PDBCREDO0.5240.2810.5240.008
Rv0467_1f8m_A363g5d_1N1_A_1PDBCREDO0.5230.2830.5230.008
Rv0467_1f8m_A361ki3_PE2_A_1PDBCREDO0.5410.2560.5200.008
Rv0467_1f8m_A362uxo_TAC_B_1211PDBCREDO0.5510.2430.5090.009
Rv0467_1f8m_A363kw2_ADN_A_300PDBCREDO0.5490.2450.5090.010
Rv0467_1f8m_A362xkw_P1B_B_1475PDBCREDO0.5890.1920.5070.010
Rv0467_1f8m_A363k2h_LYA_A_514PDBCREDO0.5040.3130.5040.010
Rv0467_1f8m_A361fk9_EFZ_A_999PDBCREDO0.5220.2850.5020.011
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
CHEMBL1209635Inhibition = 19.82 %Percent inhibition of Mycobacterium tuberculosis isocitrate lyase (ICL) at 10 uMhttp://www.ncbi.nlm.nih.gov/pubmed/20615698
CHEMBL1209699Inhibition = 46.8 %Percent inhibition of Mycobacterium tuberculosis isocitrate lyase (ICL) at 10 uMhttp://www.ncbi.nlm.nih.gov/pubmed/20615698
CHEMBL1209700Inhibition = 30.12 %Percent inhibition of Mycobacterium tuberculosis isocitrate lyase (ICL) at 10 uMhttp://www.ncbi.nlm.nih.gov/pubmed/20615698
CHEMBL1209782Inhibition = 86.8 %Percent inhibition of Mycobacterium tuberculosis isocitrate lyase (ICL) at 10 uMhttp://www.ncbi.nlm.nih.gov/pubmed/20615698
CHEMBL1209783Inhibition = 34.86 %Percent inhibition of Mycobacterium tuberculosis isocitrate lyase (ICL) at 10 uMhttp://www.ncbi.nlm.nih.gov/pubmed/20615698
CHEMBL1209784Inhibition = 48.9 %Percent inhibition of Mycobacterium tuberculosis isocitrate lyase (ICL) at 10 uMhttp://www.ncbi.nlm.nih.gov/pubmed/20615698
CHEMBL1209785Inhibition = 73.12 %Percent inhibition of Mycobacterium tuberculosis isocitrate lyase (ICL) at 10 uMhttp://www.ncbi.nlm.nih.gov/pubmed/20615698
CHEMBL1209786Inhibition = 28.13 %Percent inhibition of Mycobacterium tuberculosis isocitrate lyase (ICL) at 10 uMhttp://www.ncbi.nlm.nih.gov/pubmed/20615698
CHEMBL1209869Inhibition = 32.54 %Percent inhibition of Mycobacterium tuberculosis isocitrate lyase (ICL) at 10 uMhttp://www.ncbi.nlm.nih.gov/pubmed/20615698
CHEMBL1651581Inhibition = 18.9 %Inhibition of Mycobacterium tuberculosis isocitrate lyase at 10 mMhttp://www.ncbi.nlm.nih.gov/pubmed/21093117
CHEMBL1651585Inhibition = 15.93 %Inhibition of Mycobacterium tuberculosis isocitrate lyase at 10 mMhttp://www.ncbi.nlm.nih.gov/pubmed/21093117
CHEMBL1651595Inhibition = 6.38 %Inhibition of Mycobacterium tuberculosis isocitrate lyase at 10 mMhttp://www.ncbi.nlm.nih.gov/pubmed/21093117
CHEMBL1651596Inhibition = 18.54 %Inhibition of Mycobacterium tuberculosis isocitrate lyase at 10 mMhttp://www.ncbi.nlm.nih.gov/pubmed/21093117
CHEMBL1651597Inhibition = 28.37 %Inhibition of Mycobacterium tuberculosis isocitrate lyase at 10 mMhttp://www.ncbi.nlm.nih.gov/pubmed/21093117
CHEMBL1651598Inhibition = 11.03 %Inhibition of Mycobacterium tuberculosis isocitrate lyase at 10 mMhttp://www.ncbi.nlm.nih.gov/pubmed/21093117
CHEMBL1651599Inhibition = 9.49 %Inhibition of Mycobacterium tuberculosis isocitrate lyase at 10 mMhttp://www.ncbi.nlm.nih.gov/pubmed/21093117
CHEMBL1651605Inhibition = 23.3 %Inhibition of Mycobacterium tuberculosis isocitrate lyase at 10 mMhttp://www.ncbi.nlm.nih.gov/pubmed/21093117
CHEMBL1651617Inhibition = 63.44 %Inhibition of Mycobacterium tuberculosis isocitrate lyase at 10 mMhttp://www.ncbi.nlm.nih.gov/pubmed/21093117
CHEMBL1818286IC50 = 21.32 uMInhibition of Mycobacterium tuberculosis isocitrate lyasehttp://www.ncbi.nlm.nih.gov/pubmed/21840711
CHEMBL1818287IC50 = 32.46 uMInhibition of Mycobacterium tuberculosis isocitrate lyasehttp://www.ncbi.nlm.nih.gov/pubmed/21840711
CHEMBL1818370IC50 = 36.8 uMInhibition of Mycobacterium tuberculosis isocitrate lyasehttp://www.ncbi.nlm.nih.gov/pubmed/21840711
CHEMBL1818376IC50 = 12.6 uMInhibition of Mycobacterium tuberculosis isocitrate lyasehttp://www.ncbi.nlm.nih.gov/pubmed/21840711
CHEMBL1818377IC50 = 41.21 uMInhibition of Mycobacterium tuberculosis isocitrate lyasehttp://www.ncbi.nlm.nih.gov/pubmed/21840711
CHEMBL1818378IC50 = 30.18 uMInhibition of Mycobacterium tuberculosis isocitrate lyasehttp://www.ncbi.nlm.nih.gov/pubmed/21840711
CHEMBL1818380IC50 = 0.2 uMInhibition of Mycobacterium tuberculosis isocitrate lyasehttp://www.ncbi.nlm.nih.gov/pubmed/21840711
CHEMBL1818381IC50 = 0.12 uMInhibition of Mycobacterium tuberculosis isocitrate lyasehttp://www.ncbi.nlm.nih.gov/pubmed/21840711
CHEMBL1818382IC50 = 1.46 uMInhibition of Mycobacterium tuberculosis isocitrate lyasehttp://www.ncbi.nlm.nih.gov/pubmed/21840711
CHEMBL1818383IC50 = 0.1 uMInhibition of Mycobacterium tuberculosis isocitrate lyasehttp://www.ncbi.nlm.nih.gov/pubmed/21840711
CHEMBL451226Inhibition = 63.2 %Percent inhibition of Mycobacterium tuberculosis isocitrate lyase (ICL) at 100 uMhttp://www.ncbi.nlm.nih.gov/pubmed/20615698
CHEMBL451226IC50 = 116 uMInhibition of Mycobacterium tuberculosis isocitrate lyasehttp://www.ncbi.nlm.nih.gov/pubmed/21840711
CHEMBL451226Inhibition = 65.99 %Inhibition of Mycobacterium tuberculosis isocitrate lyase at 100 mMhttp://www.ncbi.nlm.nih.gov/pubmed/21093117
Off-target activity - ligand based from TIBLE
  View results in TIBLE page
Predicted off-targetMethodSummaryFull results
Death-associated protein kinase 1 1JKLPharmMapper0 hydroph + 9 HB + 2 pos/neg + 0 aromLink
Dual specificity mitogen-activated protein kinase kinase 1 1S9JPharmMapper7 hydroph + 2 HB + 0 pos/neg + 0 aromLink
GTPase HRas 5P21PharmMapper0 hydroph + 13 HB + 2 pos/neg + 0 aromLink
Death-associated protein kinase 1 1IG1PharmMapper0 hydroph + 11 HB + 2 pos/neg + 0 aromLink
Tyrosine-protein phosphatase non-receptor type 1 1JF7PharmMapper2 hydroph + 6 HB + 2 pos/neg + 0 aromLink
DNA gyrase subunit A [-] SEAE_value = 6.35e-33 & MaxTC = 0.56Link
DNA polymerase III polC-type [-] SEAE_value = 1.57e-17 & MaxTC = 0.54Link
DNA gyrase subunit A SEAE_value = 2.01e-16 & MaxTC = 0.54Link
Topoisomerase IV subunit A SEAE_value = 3.09e-14 & MaxTC = 0.54Link
Histone deacetylase 3 SEAE_value = 9.86e-14 & MaxTC = 0.47Link
Histone deacetylase 2 SEAE_value = 7.89e-13 & MaxTC = 0.44Link
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
glyoxylatePubChem0.99974.0355
succinatePubChem0.998118.088
isocitratePubChem0.992192.124
magnesiumPubChem0.97724.305
acetyl-CoAPubChem0.973809.571
pyruvic acidPubChem0.96888.0621
malatePubChem0.963134.087
coenzyme APubChem0.944767.534
cis-aconitatePubChem0.919174.108
Co-APubChem0.914767.534
D-malatePubChem0.9134.087
protiumPubChem0.92.01576
deuteriumPubChem0.92.01588
H(+)PubChem0.92.01588
D-isocitratePubChem0.9192.124
hydroxyl radicalsPubChem0.917.0073
hydron; succinatePubChem0.9119.096
acetyl coenzyme-APubChem0.9809.571
glycerolPubChem0.83492.0938
malonatePubChem0.833104.061
acetatePubChem0.78759.044
polyethylene glycolPubChem0.76862.0678
acetate asPubChem0.766404.497
ethylene glycol; hydronPubChem0.76563.0758
Na(+)PubChem0.76522.9898
propionyl-CoAPubChem0.744823.597
phosphoenolpyruvatePubChem0.741168.042
NADPPubChem0.716744.413
diethyl pyrocarbonatePubChem0.713162.141
itaconic acidPubChem0.7130.099