Structure of PDB 3ndv Chain B Binding Site BS01

Receptor Information
>3ndv Chain B (length=365) Species: 364098 (Sphingosinicella xenopeptidilytica) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GPRARDLGVPFEGTPGALNAITDVAGVEVGHTTVISGDGAMVIGKGPYRT
GVTIIHPLGKTSLDGVAAGRAVINGTGEWTGMHLVDEVGQFLGPIALTGT
GNVGLVHQSMMDWSVGKVPEEALFSRLLPVVAETLDNRLNDVFGHGLTRD
HVFAALDGAKGGPVAEGNVGGGTGMIAYTFKGGIGTSSRVVSAGDTRYTV
GVLVQANHGDRNDLRIAGVQIGKEIKGAWPEVNGIVAAGPDAGSLLIVIA
TDAPLMPHQLERMARRAALGVGRNGSTAGALSGEFALAFSTSHVIPLGGK
PRLPAIINDTDSETMNALFRGVVQATEEALVNQLVASETMTGANNAKVYG
IPHDQLARIMKARFP
Ligand information
Ligand IDAIC
InChIInChI=1S/C16H19N3O4S/c1-16(2)11(15(22)23)19-13(21)10(14(19)24-16)18-12(20)9(17)8-6-4-3-5-7-8/h3-7,9-11,14H,17H2,1-2H3,(H,18,20)(H,22,23)/t9-,10-,11+,14-/m1/s1
InChIKeyAVKUERGKIZMTKX-NJBDSQKTSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C2N3C(=O)C(NC(=O)C(c1ccccc1)N)C3SC2(C)C
OpenEye OEToolkits 1.5.0CC1(C(N2C(S1)C(C2=O)NC(=O)C(c3ccccc3)N)C(=O)O)C
CACTVS 3.341CC1(C)S[C@@H]2[C@H](NC(=O)[C@H](N)c3ccccc3)C(=O)N2[C@H]1C(O)=O
OpenEye OEToolkits 1.5.0CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)[C@@H](c3ccccc3)N)C(=O)O)C
CACTVS 3.341CC1(C)S[CH]2[CH](NC(=O)[CH](N)c3ccccc3)C(=O)N2[CH]1C(O)=O
FormulaC16 H19 N3 O4 S
Name(2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID;
AMPICILLIN;
D(-)-ALPHA-AMINOBENZYLPENICILLIN;
6-[D(-)-ALPHA-AMINOPHENYLLACETAMIDO]PENICILLANIC ACID
ChEMBLCHEMBL174
DrugBankDB00415
ZINCZINC000003830218
PDB chain3ndv Chain B Residue 376 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ndv Crystal structures and inhibition of the beta-aminopeptidase BapA, a new ampicillin-recognizing member of the N-terminal nucleophile hydrolase family
Resolution1.7 Å
Binding residue
(original residue number in PDB)
T76 E133 L135 R138 S250 L287
Binding residue
(residue number reindexed from 1)
T76 E133 L135 R138 S244 L281
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) L135 N207 S250 S288 G289
Catalytic site (residue number reindexed from 1) L135 N207 S244 S282 G283
Enzyme Commision number 3.4.11.25: beta-peptidyl aminopeptidase.
Gene Ontology
Molecular Function
GO:0004177 aminopeptidase activity
GO:0042802 identical protein binding
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0042597 periplasmic space

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:3ndv, PDBe:3ndv, PDBj:3ndv
PDBsum3ndv
PubMed
UniProtQ52VH2|BAPA_SPHXN Beta-peptidyl aminopeptidase BapA (Gene Name=bapA)

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