Structure of PDB 4qir Chain A Binding Site BS01

Receptor Information
>4qir Chain A (length=864) Species: 122586 (Neisseria meningitidis MC58) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TVHYLKDYQTPAYHILKTDLHFDINEPQTVVKSRLTVEPQRVGEPLVLDG
SAKLLSVKINGAAADYVLEGETLTIAGVPSERFTVEVETEILPAENKSLM
GLYASGGNLFTQCEPEGFRKITFYIDRPDVMSKFTTTIVADKKRYPVLLS
NGNKIDGGEFSDGRHWVKWEDPFSKPSYLFALVAGDLAVTEDYFTTMSGR
NVKIEFYTTEADKPKVGFAVESLKNAMKWDETRFGLEYDLDIFMVVAVGD
FNMGAMENKGLNIFNTKFVLADSRTATDTDFEGIESVVGHEYFHNWTGNR
VTCRDWFQLSLKEGLTVFRDQEFSGDRASRAVRRIENIRLLRQHQFPEDA
GPTAHPVRPASYEEMNNFYTMTVYEKGAEVVRMYHTLLGEEGFQKGMKLY
FQRHDGQAVTCDDFRAAMADANGINLDQFALWYSQAGTPVLEAEGRLKNN
IFELTVKQTVPPTPDMTDKQPMMIPVKVGLLNRNGEAVAFDYQGKRATEA
VLLLTEAEQTFLLEGVTEAVVPSLLRGFSAPVHLNYPYSDDDLLLLLAHD
SDAFTRWEAAQTLYRRAVAANLATLSDGVELPKHEKLLAAVEKVISDDLL
DNAFKALLLGVPSEAELWDGAENIDPLRYHQAREALLDTLAVHFLPKWHE
LNRQAAKQENQSYEYSPEAAGWRTLRNVCRAFVLRADPAHIETVAEKYGE
MAQNMTHEWGILSAVNGNESDTRNRLLAQFADKFSDDALVMDKYFALVGS
SRRSDTLQQVRTALQHPKFSLENPNKARSLIGSFSRNVPHFHAEDGSGYR
FIADKVIEIDRFNPQVAARLVQAFNLCNKLEPHRKNLVKQALQRIRAQEG
LSKDVGEIVGKILD
Ligand information
Ligand ID379
InChIInChI=1S/C18H23N2O4P/c19-17(9-8-15-7-4-10-20-12-15)25(23,24)13-16(18(21)22)11-14-5-2-1-3-6-14/h1-7,10,12,16-17H,8-9,11,13,19H2,(H,21,22)(H,23,24)/t16-,17-/m1/s1
InChIKeyLWRKOPLMYMXZKW-IAGOWNOFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1ccc(cc1)C[C@H](CP(=O)([C@H](CCc2cccnc2)N)O)C(=O)O
CACTVS 3.385N[CH](CCc1cccnc1)[P](O)(=O)C[CH](Cc2ccccc2)C(O)=O
CACTVS 3.385N[C@@H](CCc1cccnc1)[P](O)(=O)C[C@@H](Cc2ccccc2)C(O)=O
ACDLabs 12.01O=C(O)C(Cc1ccccc1)CP(=O)(O)C(N)CCc2cccnc2
OpenEye OEToolkits 1.7.6c1ccc(cc1)CC(CP(=O)(C(CCc2cccnc2)N)O)C(=O)O
FormulaC18 H23 N2 O4 P
Name3-{[(R)-1-amino-3-(pyridin-3-yl)propyl](hydroxy)phosphoryl}-(S)-2-benzylpropanoic acid
ChEMBL
DrugBank
ZINCZINC000098208400
PDB chain4qir Chain A Residue 901 [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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PDB4qir Structure-guided, single-point modifications in the phosphinic dipeptide structure yield highly potent and selective inhibitors of neutral aminopeptidases.
Resolution1.701 Å
Binding residue
(original residue number in PDB)		E117 M256 G257 A258 M259 E260 H293 E294 H297 E316 D323 N369 Y372 Y377
Binding residue
(residue number reindexed from 1)		E114 M253 G254 A255 M256 E257 H290 E291 H294 E313 D320 N366 Y369 Y374
Annotation score1
Binding affinityMOAD: Ki=112nM
PDBbind-CN: -logKd/Ki=6.95,Ki=112nM
Enzymatic activity
Catalytic site (original residue number in PDB) E260 H293 E294 H297 E316 N369 Y377
Catalytic site (residue number reindexed from 1) E257 H290 E291 H294 E313 N366 Y374
Enzyme Commision number 3.4.11.2: membrane alanyl aminopeptidase.
Gene Ontology
Molecular Function
GO:0004177 aminopeptidase activity
GO:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
GO:0046872 metal ion binding
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:4qir, PDBe:4qir, PDBj:4qir
PDBsum4qir
PubMed25192493
UniProtQ9JYV4

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