Structure of PDB 5yqb Chain A Binding Site BS03

Receptor Information
>5yqb Chain A (length=866) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
PQAKYRHDYRAPDYQITDIDLTFDLDAQKTVVTAVSQAVRHGASDAPLRL
NGEDLKLVSVHINDEPWTAWKEEEGALVISNLPERFTLKIINEISPAANT
ALEGLYQSGDALCTQCEAEGFRHITYYLDRPDVLARFTTKIIADKIKYPF
LLSNGNRVAQGELENGRHWVQWQDPFPKPCYLFALVAGDFDVLRDTFTTR
SGREVALELYVDRGNLDRAPWAMTSLKNSMKWDEERFGLEYDLDIYMIVA
VDFFNMGAMENKGLNIFNSKYVLARTDTATDKDYLDIERVIGHEYFHNWT
GNRVTCRDWFQLSLKEGLTVFRDQEFSSDLGSRAVNRINNVRTMRGLQFA
EDASPMAHPIRPDMVIEMNNFYTLTVYEKGAEVIRMIHTLLGEENFQKGM
QLYFERHDGSAATCDDFVQAMEDASNVDLSHFRRWYSQSGTPIVTVKDDY
NPETEQYTLTISQRTPATPDQAEKQPLHIPFAIELYDNEGKVIPLQKGGH
PVNSVLNVTQAEQTFVFDNVYFQPVPALLCEFSAPVKLEYKWSDQQLTFL
MRHARNDFSRWDAAQSLLATYIKLNVARHQQGQPLSLPVHVADAFRAVLL
DEKIDPALAAEILTLPSVNEMAELFDIIDPIAIAEVREALTRTLATELAD
ELLAIYNANYQSEYRVEHEDIAKRTLRNACLRFLAFGETHLADVLVSKQF
HEANNMTDALAALSAAVAAQLPCRDALMQEYDDKWHQNGLVMDKWFILQA
TSPAANVLETVRGLLQHRSFTMSNPNRIRSLIGAFAGSNPAAFHAEDGSG
YLFLVEMLTDLNSRNPQVASRLIEPLIRLKRYDAKRQEKMRAALEQLKGL
ENLSGDLYEKITKALA
Ligand information
Ligand IDGMC
InChIInChI=1S/C12H18N6O3/c1-17(2)10-8-11(15-4-14-10)18(5-16-8)12-9(20)7(13)6(3-19)21-12/h4-7,9,12,19-20H,3,13H2,1-2H3/t6-,7-,9-,12-/m1/s1
InChIKeyRYSMHWILUNYBFW-GRIPGOBMSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CN(C)c1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)N)O
CACTVS 3.341CN(C)c1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](N)[CH]3O
CACTVS 3.341CN(C)c1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](N)[C@H]3O
OpenEye OEToolkits 1.5.0CN(C)c1c2c(ncn1)n(cn2)C3C(C(C(O3)CO)N)O
ACDLabs 10.04n2c1c(ncnc1N(C)C)n(c2)C3OC(C(N)C3O)CO
FormulaC12 H18 N6 O3
Name(2R,3R,4S,5S)-4-AMINO-2-[6-(DIMETHYLAMINO)-9H-PURIN-9-YL]-5-(HYDROXYMETHYL)TETRAHYDRO-3-FURANOL;
6N-DIMETHYL-3'-DEOXY-AMINO-ADENOSINE
ChEMBLCHEMBL1233071
DrugBank
ZINCZINC000003875394
PDB chain5yqb Chain A Residue 903 [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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PDB5yqb Puromycin, a selective inhibitor of PSA acts as a substrate for other M1 family aminopeptidases: Biochemical and structural basis
Resolution1.56 Å
Binding residue
(original residue number in PDB)		H297 Y376 L378 Y381 R825
Binding residue
(residue number reindexed from 1)		H293 Y372 L374 Y377 R821
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E264 H297 E298 H301 E320 N373 Y381
Catalytic site (residue number reindexed from 1) E260 H293 E294 H297 E316 N369 Y377
Enzyme Commision number 3.4.11.2: membrane alanyl aminopeptidase.
Gene Ontology
Molecular Function
GO:0004177 aminopeptidase activity
GO:0005515 protein binding
GO:0008237 metallopeptidase activity
GO:0008270 zinc ion binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0005886 plasma membrane

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Molecular Function
View graph for
Biological Process
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Cellular Component
External links
PDB RCSB:5yqb, PDBe:5yqb, PDBj:5yqb
PDBsum5yqb
PubMed
UniProtP04825|AMPN_ECOLI Aminopeptidase N (Gene Name=pepN)

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