Structure of PDB 6pt1 Chain B Binding Site BS01

Receptor Information
>6pt1 Chain B (length=244) Species: 573 (Klebsiella pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FQGWQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPAST
FKIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVP
VYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQIS
FLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGW
WVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP
Ligand information
Ligand IDMER
InChIInChI=1S/C17H27N3O5S/c1-8-13(11(7-21)9(2)22)19-14(17(24)25)15(8)26-10-5-12(18-6-10)16(23)20(3)4/h7-13,18-19,22H,5-6H2,1-4H3,(H,24,25)/t8-,9-,10+,11-,12+,13-/m1/s1
InChIKeyDYQHXZPAIVAJRU-HTXLXMOSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC1C(NC(=C1SC2CC(NC2)C(=O)N(C)C)C(=O)O)C(C=O)C(C)O
CACTVS 3.370C[CH](O)[CH](C=O)[CH]1NC(=C(S[CH]2CN[CH](C2)C(=O)N(C)C)[CH]1C)C(O)=O
CACTVS 3.370C[C@@H](O)[C@@H](C=O)[C@@H]1NC(=C(S[C@@H]2CN[C@@H](C2)C(=O)N(C)C)[C@@H]1C)C(O)=O
ACDLabs 12.01O=C(O)C2=C(SC1CC(C(=O)N(C)C)NC1)C(C(N2)C(C=O)C(O)C)C
OpenEye OEToolkits 1.7.6C[C@@H]1[C@@H](NC(=C1S[C@H]2C[C@H](NC2)C(=O)N(C)C)C(=O)O)[C@H](C=O)[C@@H](C)O
FormulaC17 H27 N3 O5 S
Name(4R,5S)-3-{[(3S,5S)-5-(dimethylcarbamoyl)pyrrolidin-3-yl]sulfanyl}-5-[(2S,3R)-3-hydroxy-1-oxobutan-2-yl]-4-methyl-4,5-d ihydro-1H-pyrrole-2-carboxylic acid;
Meropenem, bound form
ChEMBL
DrugBank
ZINCZINC000103547705
PDB chain6pt1 Chain B Residue 302 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6pt1 Structural Basis for Substrate Specificity and Carbapenemase Activity of OXA-48 Class D beta-Lactamase.
Resolution2.0 Å
Binding residue
(original residue number in PDB)		S70 S118 V120 T209 G210 Y211 R250
Binding residue
(residue number reindexed from 1)		S49 S97 V99 T188 G189 Y190 R229
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S70 K73 S118 Y123 W157 Y211
Catalytic site (residue number reindexed from 1) S49 K52 S97 Y102 W136 Y190
Enzyme Commision number 3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0008658 penicillin binding
GO:0008800 beta-lactamase activity
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
Biological Process
GO:0017001 antibiotic catabolic process
GO:0046677 response to antibiotic
GO:0071555 cell wall organization

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6pt1, PDBe:6pt1, PDBj:6pt1
PDBsum6pt1
PubMed31872762
UniProtQ6XEC0

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