Structure of PDB 3pkd Chain A Binding Site BS03

Receptor Information
>3pkd Chain A (length=282) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RTALSPGVLSPTRPVPNWIARPEYVGKPAAQEGSEPWVQTPEVIEKMRVA
GRIAAGALAEAGKAVAPGVTTDELDRIAHEYLVDNGAYPSTLGYKGFPKS
CCTSLNEVICHGIPDSTVITDGDIVNIDVTAYIGGVHGDTNATFPAGDVA
DEHRLLVDRTREATMRAINTVKPGRALSVIGRVIESYANRFGYNVVRDFT
GHGIGTTFHNGLVVLHYDQPAVETIMQPGMTFTIEPMINLGALDYEIWDD
GWTVVTKDRKWTAQFEHTLLVTDTGVEILTCL
Ligand information
Ligand IDY10
InChIInChI=1S/C21H31NO5/c1-21(2,3)10-9-16(23)17(24)18(25)19(27-4)20(26)22-15-11-13-7-5-6-8-14(13)12-15/h5-10,15-19,23-25H,11-12H2,1-4H3,(H,22,26)/b10-9+/t16-,17+,18-,19-/m1/s1
InChIKeyXTHOIFAGDPGJPZ-PQQJDVFMSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CO[C@H]([C@H](O)[C@@H](O)[C@H](O)/C=C/C(C)(C)C)C(=O)NC1Cc2ccccc2C1
OpenEye OEToolkits 1.7.6CC(C)(C)C=CC(C(C(C(C(=O)NC1Cc2ccccc2C1)OC)O)O)O
OpenEye OEToolkits 1.7.6CC(C)(C)/C=C/[C@H]([C@@H]([C@H]([C@H](C(=O)NC1Cc2ccccc2C1)OC)O)O)O
CACTVS 3.370CO[CH]([CH](O)[CH](O)[CH](O)C=CC(C)(C)C)C(=O)NC1Cc2ccccc2C1
ACDLabs 12.01O=C(NC2Cc1ccccc1C2)C(OC)C(O)C(O)C(O)/C=C/C(C)(C)C
FormulaC21 H31 N O5
Name(E,2R,3R,4S,5R)-N-(2,3-dihydro-1H-inden-2-yl)-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide
ChEMBLCHEMBL1738933
DrugBank
ZINCZINC000066166121
PDB chain3pkd Chain A Residue 288 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3pkd Inhibition of Mycobacterium tuberculosis Methionine Aminopeptidases by Bengamide Derivatives.
Resolution1.47 Å
Binding residue
(original residue number in PDB)		Y97 H114 D131 D142 T203 H205 F211 H212 E238 E269
Binding residue
(residue number reindexed from 1)		Y94 H111 D128 D139 T200 H202 F208 H209 E235 E266
Annotation score1
Binding affinityMOAD: ic50=0.76uM
PDBbind-CN: -logKd/Ki=6.12,IC50=760nM
Enzymatic activity
Catalytic site (original residue number in PDB) H114 D131 D142 G204 H205 G208 H212 L215 E238 N242 E269
Catalytic site (residue number reindexed from 1) H111 D128 D139 G201 H202 G205 H209 L212 E235 N239 E266
Enzyme Commision number 3.4.11.18: methionyl aminopeptidase.
Gene Ontology
Molecular Function
GO:0004177 aminopeptidase activity
GO:0004239 initiator methionyl aminopeptidase activity
GO:0005506 iron ion binding
GO:0008235 metalloexopeptidase activity
GO:0046872 metal ion binding
GO:0046914 transition metal ion binding
GO:0050897 cobalt ion binding
GO:0070006 metalloaminopeptidase activity
Biological Process
GO:0006508 proteolysis
GO:0016485 protein processing
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3pkd, PDBe:3pkd, PDBj:3pkd
PDBsum3pkd
PubMed21465667
UniProtP9WK19|MAP12_MYCTU Methionine aminopeptidase 2 (Gene Name=map)

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