Rv0429c

Tuberculist information
Gene namedef
Protein functionProbable polypeptide deformylase Def (PDF) (formylmethionine deformylase)
Functional category(tuberculist)information pathways
Gene location(kb)517.803
Molecular mass(da)20938.7
External sites TB Database TubercuList WebTB
Protein sequence
Number of amino acids : 197
	  		  	1    MAVVPIRIVGDPVLHTATTPVTVAADGSLPADLAQLIATMYDTMDAANGVGLAANQIGCS   60
			  	61   LRLFVYDCAADRAMTARRRGVVINPVLETSEIPETMPDPDTDDEGCLSVPGESFPTGRAK  120
			  	121  WARVTGLDADGSPVSIEGTGLFARMLQHETGHLDGFLYLDRLIGRYARNAKRAVKSHGWG  180
			  	181  VPGLSWLPGEDPDPFGH

Known structures in the PDB
PDB ID3E3U
Total residue count197
Number of chains1
MethodX-RAY
Resolution1.56
1 20 39 58 77 96 115 134 153 172 191 Range: 3 to 168  |  Coverage: 83% Pep_deformylase Range: 2 to 197  |  Coverage: 98% 1 Range: 1 to 177  |  Coverage: 89% 2 Range: 1 to 197  |  Coverage: 99% 1
Number of amino acids : 197
Domains assigned based on sequence. Mtb Structural proteome models CHOPIN models
Profile-based domain assignment
Structural/Functional domain familyPfam acc.no./SCOP IDDomain Region
Pep_deformylasePF013273-168
Mtb Structural Proteome models
Model Number1
Model nameRv0429c_3e3u_A
Template3E3U    APDBCREDO
Template coverage2_197
Template Identity(%)100.0
Model coverage(%)99.0
Normalized DOPE score-1.716

Model Number2
Model nameRv0429c
Template1N5N    APDBCREDO
Template coverage1_164
Template Identity(%)40.9
Model coverage(%)89.3
Normalized DOPE score-0.624

Structure Models from Chopin
Model Number1
Profiled.167.1.1 - 3.90.45.10
Click for model details
zscore27.35
Residue begin1
Residue end197
Binding pockets
STRING
Cytoscape Web will replace the contents of this div with protein-protein interaction network.
Protein interacting with Rv0429cGene nameConfidence Score
Rv1406fmt0.98
Rv1406fmt0.98
Rv1389gmk0.939
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
CHEMBL443904IC50 = 0.01 uMInhibition of Mycobacterium tuberculosis peptide deformylase expressed in Escherichia coli M15(pREp4) by microplate assayhttp://www.ncbi.nlm.nih.gov/pubmed/19008098
CHEMBL463859IC50 = 0.021 uMInhibition of Mycobacterium tuberculosis peptide deformylase expressed in Escherichia coli M15(pREp4) by microplate assayhttp://www.ncbi.nlm.nih.gov/pubmed/19008098
CHEMBL464050IC50 = 0.803 uMInhibition of Mycobacterium tuberculosis peptide deformylase expressed in Escherichia coli M15(pREp4) by microplate assayhttp://www.ncbi.nlm.nih.gov/pubmed/19008098
CHEMBL464060IC50 = 0.018 uMInhibition of Mycobacterium tuberculosis peptide deformylase expressed in Escherichia coli M15(pREp4) by microplate assayhttp://www.ncbi.nlm.nih.gov/pubmed/19008098
CHEMBL465740IC50 = 0.013 uMInhibition of Mycobacterium tuberculosis peptide deformylase expressed in Escherichia coli M15(pREp4) by microplate assayhttp://www.ncbi.nlm.nih.gov/pubmed/19008098
CHEMBL480220IC50 = 0.028 uMInhibition of Mycobacterium tuberculosis peptide deformylase expressed in Escherichia coli M15(pREp4) by microplate assayhttp://www.ncbi.nlm.nih.gov/pubmed/19008098
CHEMBL481391IC50 = 0.068 uMInhibition of Mycobacterium tuberculosis peptide deformylase expressed in Escherichia coli M15(pREp4) by microplate assayhttp://www.ncbi.nlm.nih.gov/pubmed/19008098
CHEMBL482179IC50 = 0.024 uMInhibition of Mycobacterium tuberculosis peptide deformylase expressed in Escherichia coli M15(pREp4) by microplate assayhttp://www.ncbi.nlm.nih.gov/pubmed/19008098
CHEMBL482180IC50 = 0.015 uMInhibition of Mycobacterium tuberculosis peptide deformylase expressed in Escherichia coli M15(pREp4) by microplate assayhttp://www.ncbi.nlm.nih.gov/pubmed/19008098
CHEMBL506131IC50 = 0.202 uMInhibition of Mycobacterium tuberculosis peptide deformylase expressed in Escherichia coli M15(pREp4) by microplate assayhttp://www.ncbi.nlm.nih.gov/pubmed/19008098
CHEMBL506649IC50 = 0.013 uMInhibition of Mycobacterium tuberculosis peptide deformylase expressed in Escherichia coli M15(pREp4) by microplate assayhttp://www.ncbi.nlm.nih.gov/pubmed/19008098
CHEMBL517164IC50 = 0.049 uMInhibition of Mycobacterium tuberculosis peptide deformylase expressed in Escherichia coli M15(pREp4) by microplate assayhttp://www.ncbi.nlm.nih.gov/pubmed/19008098
CHEMBL518077IC50 = 0.161 uMInhibition of Mycobacterium tuberculosis peptide deformylase expressed in Escherichia coli M15(pREp4) by microplate assayhttp://www.ncbi.nlm.nih.gov/pubmed/19008098
CHEMBL519613IC50 = 0.008 uMInhibition of Mycobacterium tuberculosis peptide deformylase expressed in Escherichia coli M15(pREp4) by microplate assayhttp://www.ncbi.nlm.nih.gov/pubmed/19008098
CDD-341893NoneNoneNone
CDD-341898NoneNoneNone
CDD-341902NoneNoneNone
CDD-341903NoneNoneNone
Off-target activity - ligand based from TIBLE
  View results in TIBLE page
Predicted off-targetMethodSummaryFull results
Glutathione S-transferase theta-2 1LJRPharmMapper1 hydroph + 4 HB + 2 pos/neg + 0 aromLink
Leukotriene A-4 hydrolase 1HS6PharmMapper3 hydroph + 3 HB + 3 pos/neg + 0 aromLink
Leukocyte elastase 1HNEPharmMapper3 hydroph + 6 HB + 0 pos/neg + 0 aromLink
Heat shock protein HSP 90-alpha 2QG0PharmMapper3 hydroph + 4 HB + 0 pos/neg + 0 aromLink
Serum albumin 1HK1PharmMapper4 hydroph + 2 HB + 1 pos/neg + 0 aromLink
matrilysin; matrix metalloprotease-7 SEAE_value = 2.43e-75 & MaxTC = 0.6Link
peptide deformylase SEAE_value = 2.56e-75 & MaxTC = 0.6Link
Purinergic receptor P2Y12 SEAE_value = 1.2e-45 & MaxTC = 0.34Link
Angiotensin-converting enzyme SEAE_value = 9.99e-43 & MaxTC = 0.42Link
peptide deformylase [-] SEAE_value = 2.85e-41 & MaxTC = 0.56Link
Trypsin I SEAE_value = 4.07e-39 & MaxTC = 0.39Link
Thrombin SEAE_value = 5.83e-36 & MaxTC = 0.4Link
peptide deformylase [-] SEAE_value = 2.87e-33 & MaxTC = 0.45Link
Angiotensin-converting enzyme SEAE_value = 1.25e-32 & MaxTC = 0.38Link
Leukocyte elastase SEAE_value = 2.24e-25 & MaxTC = 0.41Link
Prolyl-Peptidyl Isomerase Inhibitor SEAE_value = 1.18e-22 & MaxTC = 0.38Link
Angiotensin-converting enzyme SEAE_value = 2.88e-21 & MaxTC = 0.38Link
Mu opioid receptor SEAE_value = 5.65e-21 & MaxTC = 0.48Link
Plasminogen SEAE_value = 1.34e-19 & MaxTC = 0.33Link
Orexin receptor 1 SEAE_value = 6.05e-18 & MaxTC = 0.38Link
Orexin receptor 2 SEAE_value = 2.62e-16 & MaxTC = 0.39Link
Delta opioid receptor SEAE_value = 7.86e-15 & MaxTC = 0.47Link
Trypsin I SEAE_value = 7.9e-15 & MaxTC = 0.38Link
Dipeptidyl peptidase IV SEAE_value = 1.97e-14 & MaxTC = 0.35Link
FK506-binding protein 1A SEAE_value = 1.97e-13 & MaxTC = 0.32Link
Dipeptidyl peptidase VIII SEAE_value = 3.76e-11 & MaxTC = 0.36Link
Matrix metalloproteinase 3 SEAE_value = 5.23e-11 & MaxTC = 0.41Link
Poly [ADP-ribose] polymerase-1 SEAE_value = 5.24e-11 & MaxTC = 0.41Link
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
nickelPubChem0.98558.6934
formatePubChem0.98345.0174
actinoninPubChem0.981385.498
NVCPubChem0.979359.419
fMetPubChem0.977177.221
N-formylmethioninePubChem0.974177.221
BB-3497PubChem0.957329.435
zincPubChem0.92565.409
hydroxyl radicalsPubChem0.91817.0073
L-methioninePubChem0.916149.211
cobaltPubChem0.894117.866
an aldehydePubChem0.88730.026
Fe(III)PubChem0.81355.845
methanolPubChem0.80330.026
cysteatePubChem0.774169.156
cysteic acidPubChem0.774169.156
chloridePubChem0.7635.453
formylPubChem0.73429.018
nevirapinePubChem0.714266.298