Structure of PDB 6qeg Chain A Binding Site BS01

Receptor Information
>6qeg Chain A (length=364) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQ
ASEEIWNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKE
NGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRI
IDCAFTVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMES
YEVEIDGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIVKGGEATRMEEGEV
YAIETFGSTGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENF
GTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEH
TILLRPTCKEVVSR
Ligand information
Ligand IDK4K
InChIInChI=1S/C17H18N2O3S/c20-15(18-10-8-14-7-4-12-23-14)17(22)9-11-19(16(17)21)13-5-2-1-3-6-13/h1-7,12,22H,8-11H2,(H,18,20)/t17-/m0/s1
InChIKeyFZATYXICMFSLHR-KRWDZBQOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)N2CCC(C2=O)(C(=O)NCCc3cccs3)O
OpenEye OEToolkits 2.0.7c1ccc(cc1)N2CC[C@@](C2=O)(C(=O)NCCc3cccs3)O
CACTVS 3.385O[C]1(CCN(C1=O)c2ccccc2)C(=O)NCCc3sccc3
CACTVS 3.385O[C@@]1(CCN(C1=O)c2ccccc2)C(=O)NCCc3sccc3
FormulaC17 H18 N2 O3 S
Name(3~{S})-3-oxidanyl-2-oxidanylidene-1-phenyl-~{N}-(2-thiophen-2-ylethyl)pyrrolidine-3-carboxamide
ChEMBLCHEMBL4566670
DrugBank
ZINC
PDB chain6qeg Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6qeg Discovery and Structure-Based Optimization of Next-Generation Reversible Methionine Aminopeptidase-2 (MetAP-2) Inhibitors.
Resolution2.08 Å
Binding residue
(original residue number in PDB)		F219 A230 H231 D251 D262 L328 N329 H331 I338 H339 E364 Y444 E459
Binding residue
(residue number reindexed from 1)		F109 A120 H121 D141 D152 L218 N219 H221 I228 H229 E254 Y334 E349
Annotation score1
Binding affinityMOAD: ic50=0.05uM
PDBbind-CN: -logKd/Ki=7.30,IC50=0.05uM
BindingDB: IC50=50nM
Enzymatic activity
Catalytic site (original residue number in PDB) D251 D262 H331 H339 E364 E459
Catalytic site (residue number reindexed from 1) D141 D152 H221 H229 E254 E349
Enzyme Commision number 3.4.11.18: methionyl aminopeptidase.
Gene Ontology
Molecular Function
GO:0070006 metalloaminopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6qeg, PDBe:6qeg, PDBj:6qeg
PDBsum6qeg
PubMed30939017
UniProtP50579|MAP2_HUMAN Methionine aminopeptidase 2 (Gene Name=METAP2)

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