Structure of PDB 2xyd Chain A Binding Site BS01

Receptor Information
>2xyd Chain A (length=607) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LDPGLQPGQFSADEAGAQLFAQSYQSSAEQVLFQSVAASWAHDTNITAEN
ARRQEEAALLSQEFAEAWGQKAKELYEPIWQQFTDPQLRRIIGAVRTLGS
ANLPLAKRQQYNALLSQMSRIYSTAKVCLTATCWSLDPDLTNILASSRSY
AMLLFAWEGWHNAAGIPLKPLYEDFTALSNEAYKQDGFTDTGAYWRSWYN
SPTFEDDLEHLYQQLEPLYLNLHAFVRRALHRRYGDRYINLRGPIPAHLL
GDMWAQSWENIYDMVVPFPDKPNLDVTSTMLQQGWQATHMFRVAEEFFTS
LELSPMPPEFWEGSMLEKPADGREVVCHASAWDFYNRKDFRIKQCTRVTM
DQLSTVHHEMGHIQYYLQYKDLPVSLRRGANPGFHEAIGDVLALSVSTPE
HLHKIGLLDRVTNDTESDINYLLKMALEKIAFLPFGYLVDQWRWGVFSGR
TPPSRYNFDWWYLRTKYQGICPPVTRNETHFDAGAKFHVPNVTPYIRYFV
SFVLQFQFHEALCKEAGYEGPLHQCDIYRSTKAGAKLRKVLRAGSSRPWQ
EVLKDMVGLDALDAQPLLKYFQLVTQWLQEQNQQNGEVLGWPEYQWHPPL
PDNYPEG
Ligand information
Ligand ID3ES
InChIInChI=1S/C38H38N3O9P/c42-31-18-16-27(17-19-31)20-34(37(44)45)39-36(43)30(22-32-23-33(41-50-32)29-14-8-3-9-15-29)25-51(47,48)35(21-26-10-4-1-5-11-26)40-38(46)49-24-28-12-6-2-7-13-28/h1-19,23,30,34-35,42H,20-22,24-25H2,(H,39,43)(H,40,46)(H,44,45)(H,47,48)/t30-,34-,35+/m0/s1
InChIKeyZPFSKFCSVXPMBD-PFESQZPFSA-N
SMILES
SoftwareSMILES
CACTVS 3.352OC(=O)[CH](Cc1ccc(O)cc1)NC(=O)[CH](Cc2onc(c2)c3ccccc3)C[P](O)(=O)[CH](Cc4ccccc4)NC(=O)OCc5ccccc5
CACTVS 3.352OC(=O)[C@H](Cc1ccc(O)cc1)NC(=O)[C@@H](Cc2onc(c2)c3ccccc3)C[P](O)(=O)[C@H](Cc4ccccc4)NC(=O)OCc5ccccc5
OpenEye OEToolkits 1.6.1c1ccc(cc1)CC(NC(=O)OCc2ccccc2)P(=O)(CC(Cc3cc(no3)c4ccccc4)C(=O)NC(Cc5ccc(cc5)O)C(=O)O)O
OpenEye OEToolkits 1.6.1c1ccc(cc1)C[C@H](NC(=O)OCc2ccccc2)[P@](=O)(C[C@H](Cc3cc(no3)c4ccccc4)C(=O)N[C@@H](Cc5ccc(cc5)O)C(=O)O)O
FormulaC38 H38 N3 O9 P
Name[(2S)-2-({3-[HYDROXYL(2-PHENYL-(1R)-1-{[(BENZYLOXY)[(2S)-2-({3-[HYDROXYL(2-PHENYL-(1R)-1-CARBONYL]-AMINO}ETHYL)PHOSPHINYL]-2-[(3-PHENYLISOXAZOL-5-YL)METHYL]-1-OXO-PROPYL}AMINO)-3-(4-HYDROXY-PHENYL)
ChEMBLCHEMBL570953
DrugBank
ZINC
PDB chain2xyd Chain A Residue 1611 [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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PDB2xyd Novel Mechanism of Inhibition of Human Angiotensin-I-Converting Enzyme (Ace) by a Highly Specific Phosphinic Tripeptide.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		Q259 H331 A332 S333 T358 H361 E362 H365 Y369 H388 E389 D393 F435 K489 F490 H491 T496 Y498 Y501 F505
Binding residue
(residue number reindexed from 1)		Q256 H328 A329 S330 T355 H358 E359 H362 Y366 H385 E386 D390 F432 K486 F487 H488 T493 Y495 Y498 F502
Annotation score1
Binding affinityMOAD: Ki=150nM
PDBbind-CN: -logKd/Ki=6.82,Ki=150nM
BindingDB: Ki=0.65nM
Enzymatic activity
Catalytic site (original residue number in PDB) H331 A332 H361 E362 H365 E389 H491 Y501
Catalytic site (residue number reindexed from 1) H328 A329 H358 E359 H362 E386 H488 Y498
Enzyme Commision number 3.4.15.1: peptidyl-dipeptidase A.
Gene Ontology
Molecular Function
GO:0008237 metallopeptidase activity
GO:0008241 peptidyl-dipeptidase activity
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0016020 membrane

View graph for
Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2xyd, PDBe:2xyd, PDBj:2xyd
PDBsum2xyd
PubMed21352096
UniProtP12821|ACE_HUMAN Angiotensin-converting enzyme (Gene Name=ACE)

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