Structure of PDB 3nfb Chain D Binding Site BS03

Receptor Information
>3nfb Chain D (length=364) 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
GVLVQANHGDRNDLRIAGVQIGKEIKGAWPEVIVAAGPDAGKSLLIVIAT
DAPLMPHQLERMARRAALGVGRNGSTAGALSGEFALAFSTSHVIPLGGKP
RLPAIINDTDSETMNALFRGVVQATEEALVNQLVASETMTGANNAKVYGI
PHDQLARIMKARFP
Ligand information
Ligand IDOAE
InChIInChI=1S/C16H21N3O5S/c1-16(2)11(15(23)24)19-13(25-16)10(14(21)22)18-12(20)9(17)8-6-4-3-5-7-8/h3-7,9-11,13,19H,17H2,1-2H3,(H,18,20)(H,21,22)(H,23,24)/t9-,10+,11+,13+/m1/s1
InChIKeyKDAWOPKDXRJNHV-BLFANLJRSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(NC(C(=O)O)C1SC(C(N1)C(=O)O)(C)C)C(c2ccccc2)N
OpenEye OEToolkits 1.7.0CC1(C(NC(S1)C(C(=O)O)NC(=O)C(c2ccccc2)N)C(=O)O)C
OpenEye OEToolkits 1.7.0CC1([C@@H](N[C@@H](S1)[C@@H](C(=O)O)NC(=O)[C@@H](c2ccccc2)N)C(=O)O)C
CACTVS 3.370CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC(=O)[CH](N)c2ccccc2)C(O)=O
CACTVS 3.370CC1(C)S[C@H](N[C@H]1C(O)=O)[C@H](NC(=O)[C@H](N)c2ccccc2)C(O)=O
FormulaC16 H21 N3 O5 S
Name(2S,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000034064296
PDB chain3nfb Chain D Residue 375 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3nfb Crystal structure and inhibition of the beta-aminopeptidase BapA, a new ampicillin-recognizing member of the N-terminal nucleophile hydrolase family
Resolution1.85 Å
Binding residue
(original residue number in PDB)		R138 A237 A238
Binding residue
(residue number reindexed from 1)		R138 A235 A236
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 S243 S281 G282
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:3nfb, PDBe:3nfb, PDBj:3nfb
PDBsum3nfb
PubMed
UniProtQ52VH2|BAPA_SPHXN Beta-peptidyl aminopeptidase BapA (Gene Name=bapA)

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