Structure of PDB 3pkb Chain A Binding Site BS01

Receptor Information
>3pkb Chain A (length=284) Species: 1773 (Mycobacterium tuberculosis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PSRTALSPGVLSPTRPVPNWIARPEYVGKPAAQEGSEPWVQTPEVIEKMR
VAGRIAAGALAEAGKAVAPGVTTDELDRIAHEYLVDNGAYPSTLGYKGFP
KSCCTSLNEVICHGIPDSTVITDGDIVNIDVTAYIGGVHGDTNATFPAGD
VADEHRLLVDRTREATMRAINTVKPGRALSVIGRVIESYANRFGYNVVRD
FTGHGIGTTFHNGLVVLHYDQPAVETIMQPGMTFTIEPMINLGALDYEIW
DDGWTVVTKDRKWTAQFEHTLLVTDTGVEILTCL
Ligand information
Ligand IDY16
InChIInChI=1S/C14H26N2O6/c1-14(2,3)6-5-8(17)10(19)11(20)12(22-4)13(21)16-7-9(15)18/h5-6,8,10-12,17,19-20H,7H2,1-4H3,(H2,15,18)(H,16,21)/b6-5+/t8-,10+,11-,12-/m1/s1
InChIKeyAVLHKXXFCITIMH-JXTMJACFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)(C)C=CC(C(C(C(C(=O)NCC(=O)N)OC)O)O)O
ACDLabs 12.01O=C(NCC(=O)N)C(OC)C(O)C(O)C(O)/C=C/C(C)(C)C
OpenEye OEToolkits 1.7.6CC(C)(C)/C=C/[C@H]([C@@H]([C@H]([C@H](C(=O)NCC(=O)N)OC)O)O)O
CACTVS 3.370CO[C@H]([C@H](O)[C@@H](O)[C@H](O)\C=C\C(C)(C)C)C(=O)NCC(N)=O
CACTVS 3.370CO[CH]([CH](O)[CH](O)[CH](O)C=CC(C)(C)C)C(=O)NCC(N)=O
FormulaC14 H26 N2 O6
Name(E,2R,3R,4S,5R)-N-(2-azanyl-2-oxidanylidene-ethyl)-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide
ChEMBLCHEMBL1738934
DrugBank
ZINCZINC000066156877
PDB chain3pkb Chain A Residue 286 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3pkb Inhibition of Mycobacterium tuberculosis Methionine Aminopeptidases by Bengamide Derivatives.
Resolution1.25 Å
Binding residue
(original residue number in PDB)		Y97 H114 D131 D142 F202 T203 H205 H212 E238 E269
Binding residue
(residue number reindexed from 1)		Y96 H113 D130 D141 F201 T202 H204 H211 E237 E268
Annotation score1
Binding affinityMOAD: ic50=0.62uM
PDBbind-CN: -logKd/Ki=6.21,IC50=620nM
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) H113 D130 D141 G203 H204 G207 H211 L214 E237 N241 E268
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:3pkb, PDBe:3pkb, PDBj:3pkb
PDBsum3pkb
PubMed21465667
UniProtP9WK19|MAP12_MYCTU Methionine aminopeptidase 2 (Gene Name=map)

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