Structure of PDB 5lyw Chain A Binding Site BS01

Receptor Information
>5lyw Chain A (length=359) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KVQTDPPSVPICDLYPNGVFPKGQECEYPTAAWRTTSEEKKALDQASEEI
WNDFREAAEAHRQVRKYVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNA
GLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDICKIDFGTHISGRIIDCAF
TVTFNPKYDTLLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEI
DGKTYQVKPIRNLNGHSIGQYRIHAGKTVPIVKGATRMEEGEVYAIETFG
STGKGVVHDDMECSHYMKNFDVGHVPIRLPRTKHLLNVINENFGTLAFCR
RWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYTAQFEHTILLRPT
CKEVVSRGD
Ligand information
Ligand ID7BH
InChIInChI=1S/C17H19N5O/c1-12-5-2-3-7-14(12)23-9-13-6-4-8-22(13)17-15-16(19-10-18-15)20-11-21-17/h2-3,5,7,10-11,13H,4,6,8-9H2,1H3,(H,18,19,20,21)/t13-/m1/s1
InChIKeySXTKECRQJMUZOI-CYBMUJFWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cc1ccccc1OC[C@H]2CCCN2c3c4c(nc[nH]4)ncn3
CACTVS 3.385Cc1ccccc1OC[C@H]2CCCN2c3ncnc4nc[nH]c34
OpenEye OEToolkits 2.0.6Cc1ccccc1OCC2CCCN2c3c4c(nc[nH]4)ncn3
CACTVS 3.385Cc1ccccc1OC[CH]2CCCN2c3ncnc4nc[nH]c34
FormulaC17 H19 N5 O
Name6-[(2~{R})-2-[(2-methylphenoxy)methyl]pyrrolidin-1-yl]-7~{H}-purine
ChEMBLCHEMBL4097198
DrugBank
ZINC
PDB chain5lyw Chain A Residue 501 [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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PDB5lyw Novel reversible methionine aminopeptidase-2 (MetAP-2) inhibitors based on purine and related bicyclic templates.
Resolution1.69 Å
Binding residue
(original residue number in PDB)		F219 H231 D251 D262 H331 I338 H339 M384 Y444
Binding residue
(residue number reindexed from 1)		F104 H116 D136 D147 H216 I223 H224 M267 Y327
Annotation score1
Binding affinityMOAD: ic50=0.7uM
PDBbind-CN: -logKd/Ki=6.15,IC50=0.7uM
Enzymatic activity
Catalytic site (original residue number in PDB) D251 D262 H331 H339 E364 E459
Catalytic site (residue number reindexed from 1) D136 D147 H216 H224 E247 E342
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
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Biological Process
External links
PDB RCSB:5lyw, PDBe:5lyw, PDBj:5lyw
PDBsum5lyw
PubMed27998678
UniProtP50579|MAP2_HUMAN Methionine aminopeptidase 2 (Gene Name=METAP2)

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