Structure of PDB 6qef Chain A Binding Site BS01

Receptor Information
>6qef Chain A (length=365) 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
TILLRPTCKEVVSRG
Ligand information
Ligand IDHZW
InChIInChI=1S/C18H16ClFN2O3/c19-13-8-12(9-14(20)10-13)11-21-16(23)18(25)6-7-22(17(18)24)15-4-2-1-3-5-15/h1-5,8-10,25H,6-7,11H2,(H,21,23)/t18-/m0/s1
InChIKeyGYXUHDDOWYYRFT-SFHVURJKSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O[C]1(CCN(C1=O)c2ccccc2)C(=O)NCc3cc(F)cc(Cl)c3
OpenEye OEToolkits 2.0.6c1ccc(cc1)N2CCC(C2=O)(C(=O)NCc3cc(cc(c3)Cl)F)O
OpenEye OEToolkits 2.0.6c1ccc(cc1)N2CC[C@@](C2=O)(C(=O)NCc3cc(cc(c3)Cl)F)O
CACTVS 3.385O[C@@]1(CCN(C1=O)c2ccccc2)C(=O)NCc3cc(F)cc(Cl)c3
FormulaC18 H16 Cl F N2 O3
Name(3~{S})-~{N}-[(3-chloranyl-5-fluoranyl-phenyl)methyl]-3-oxidanyl-2-oxidanylidene-1-phenyl-pyrrolidine-3-carboxamide
ChEMBLCHEMBL4552396
DrugBank
ZINC
PDB chain6qef Chain A Residue 507 [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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PDB6qef Discovery and Structure-Based Optimization of Next-Generation Reversible Methionine Aminopeptidase-2 (MetAP-2) Inhibitors.
Resolution1.79 Å
Binding residue
(original residue number in PDB)		F219 H231 D251 D262 L328 N329 H331 I338 H339 E364 H382 A414 Y444 E459
Binding residue
(residue number reindexed from 1)		F109 H121 D141 D152 L218 N219 H221 I228 H229 E254 H272 A304 Y334 E349
Annotation score1
Binding affinityMOAD: ic50=0.06uM
PDBbind-CN: -logKd/Ki=7.22,IC50=0.06uM
BindingDB: IC50=60nM
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:6qef, PDBe:6qef, PDBj:6qef
PDBsum6qef
PubMed30939017
UniProtP50579|MAP2_HUMAN Methionine aminopeptidase 2 (Gene Name=METAP2)

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