Structure of PDB 3pka Chain A Binding Site BS03

Receptor Information
>3pka 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 IDY02
InChIInChI=1S/C23H37NO6/c1-14-12-15(2)20(16(3)13-14)30-11-10-24-22(28)21(29-7)19(27)18(26)17(25)8-9-23(4,5)6/h8-9,12-13,17-19,21,25-27H,10-11H2,1-7H3,(H,24,28)/b9-8+/t17-,18+,19-,21-/m1/s1
InChIKeyUMRMEUOEFMNZRM-SWQIVCBNSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0Cc1cc(c(c(c1)C)OCCNC(=O)C(C(C(C(C=CC(C)(C)C)O)O)O)OC)C
OpenEye OEToolkits 1.7.0Cc1cc(c(c(c1)C)OCCNC(=O)[C@@H]([C@@H]([C@H]([C@@H](/C=C/C(C)(C)C)O)O)O)OC)C
CACTVS 3.370CO[C@H]([C@H](O)[C@@H](O)[C@H](O)\C=C\C(C)(C)C)C(=O)NCCOc1c(C)cc(C)cc1C
CACTVS 3.370CO[CH]([CH](O)[CH](O)[CH](O)C=CC(C)(C)C)C(=O)NCCOc1c(C)cc(C)cc1C
ACDLabs 12.01O=C(NCCOc1c(cc(cc1C)C)C)C(OC)C(O)C(O)C(O)/C=C/C(C)(C)C
FormulaC23 H37 N O6
Name(2R,3R,4S,5R,6E)-3,4,5-trihydroxy-2-methoxy-8,8-dimethyl-N-[2-(2,4,6-trimethylphenoxy)ethyl]non-6-enamide
ChEMBLCHEMBL1738931
DrugBank
ZINCZINC000066165977
PDB chain3pka Chain A Residue 288 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3pka Inhibition of Mycobacterium tuberculosis Methionine Aminopeptidases by Bengamide Derivatives.
Resolution1.25 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)		Y96 H113 D130 D141 T202 H204 F210 H211 E237 E268
Annotation score1
Binding affinityMOAD: ic50=0.54uM
PDBbind-CN: -logKd/Ki=6.27,IC50=540nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3pka, PDBe:3pka, PDBj:3pka
PDBsum3pka
PubMed21465667
UniProtP9WK19|MAP12_MYCTU Methionine aminopeptidase 2 (Gene Name=map)

[Back to BioLiP]