Structure of PDB 5dyf Chain A Binding Site BS02

Receptor Information
>5dyf Chain A (length=865) Species: 122586 (Neisseria meningitidis MC58) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTVHYLKDYQTPAYHILKTDLHFDINEPQTVVKSRLTVEPQRVGEPLVLD
GSAKLLSVKINGAAADYVLEGETLTIAGVPSERFTVEVETEILPAENKSL
MGLYASGGNLFTQCEPEGFRKITFYIDRPDVMSKFTTTIVADKKRYPVLL
SNGNKIDGGEFSDGRHWVKWEDPFSKPSYLFALVAGDLAVTEDYFTTMSG
RNVKIEFYTTEADKPKVGFAVESLKNAMKWDETRFGLEYDLDIFMVVAVG
DFNMGAMENKGLNIFNTKFVLADSRTATDTDFEGIESVVGHEYFHNWTGN
RVTCRDWFQLSLKEGLTVFRDQEFSGDRASRAVRRIENIRLLRQHQFPED
AGPTAHPVRPASYEEMNNFYTMTVYEKGAEVVRMYHTLLGEEGFQKGMKL
YFQRHDGQAVTCDDFRAAMADANGINLDQFALWYSQAGTPVLEAEGRLKN
NIFELTVKQTVPPTPDMTDKQPMMIPVKVGLLNRNGEAVAFDYQGKRATE
AVLLLTEAEQTFLLEGVTEAVVPSLLRGFSAPVHLNYPYSDDDLLLLLAH
DSDAFTRWEAAQTLYRRAVAANLATLSDGVELPKHEKLLAAVEKVISDDL
LDNAFKALLLGVPSEAELWDGAENIDPLRYHQAREALLDTLAVHFLPKWH
ELNRQAAKQENQSYEYSPEAAGWRTLRNVCRAFVLRADPAHIETVAEKYG
EMAQNMTHEWGILSAVNGNESDTRNRLLAQFADKFSDDALVMDKYFALVG
SSRRSDTLQQVRTALQHPKFSLENPNKARSLIGSFSRNVPHFHAEDGSGY
RFIADKVIEIDRFNPQVAARLVQAFNLCNKLEPHRKNLVKQALQRIRAQE
GLSKDVGEIVGKILD
Ligand information
Ligand ID5HR
InChIInChI=1S/C9H15N2O3P/c10-9(15(12,13)14)7-11-6-8-4-2-1-3-5-8/h1-5,9,11H,6-7,10H2,(H2,12,13,14)/t9-/m1/s1
InChIKeyTYSJLDXCWVWYDI-SECBINFHSA-N
SMILES
SoftwareSMILES
CACTVS 3.385N[CH](CNCc1ccccc1)[P](O)(O)=O
ACDLabs 12.01N(Cc1ccccc1)CC(P(=O)(O)O)N
CACTVS 3.385N[C@@H](CNCc1ccccc1)[P](O)(O)=O
OpenEye OEToolkits 1.9.2c1ccc(cc1)CNC[C@H](N)P(=O)(O)O
OpenEye OEToolkits 1.9.2c1ccc(cc1)CNCC(N)P(=O)(O)O
FormulaC9 H15 N2 O3 P
Name[(1R)-1-amino-2-(benzylamino)ethyl]phosphonic acid
ChEMBL
DrugBank
ZINC
PDB chain5dyf Chain A Residue 912 [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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PDB5dyf The crystal structure of Aminopeptidase N in complex with N-benzyl-1,2-diaminoethylphosphonic acid
Resolution1.854 Å
Binding residue
(original residue number in PDB)		M103 Q115 E117 M256 A258 M259 E260 H293 E294 H297 E316 N369 Y377 Q818
Binding residue
(residue number reindexed from 1)		M101 Q113 E115 M254 A256 M257 E258 H291 E292 H295 E314 N367 Y375 Q816
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E260 H293 E294 H297 E316 N369 Y377
Catalytic site (residue number reindexed from 1) E258 H291 E292 H295 E314 N367 Y375
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:5dyf, PDBe:5dyf, PDBj:5dyf
PDBsum5dyf
PubMed
UniProtQ9JYV4

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