Structure of PDB 6xd7 Chain A Binding Site BS01

Receptor Information
>6xd7 Chain A (length=266) Species: 573 (Klebsiella pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LTNLVAEPFAKLEQDFGGSIGVYAMDTGSGATVSYRAEERFPLCSSFKGF
LAAAVLARSQQQAGLLDTPIRYGKNALVPWSPISEKYLTTGMTVAELSAA
AVQYSDNAAANLLLKELGGPAGLTAFMRSIGDTTFRLDRWELELASAIPG
DARDTSSPRAVTESLQKLTLGSALAAPQRQQFVDWLKGNTTGNHRIRAAV
PADWAVGDKTGTCGVYGTANDYAVVWPTGRAPIVLAVYTRAPNKDDKHSE
AVIAAAARLALEGLGV
Ligand information
Ligand IDZZ7
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-MPPDQPJWSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CC1(C)S[C@@H](N[C@H]1C(O)=O)[C@H](NC(=O)[C@H](N)c2ccccc2)C(O)=O
ACDLabs 10.04O=C(NC(C(=O)O)C1SC(C(N1)C(=O)O)(C)C)C(c2ccccc2)N
OpenEye OEToolkits 1.6.1CC1(C(NC(S1)C(C(=O)O)NC(=O)C(c2ccccc2)N)C(=O)O)C
OpenEye OEToolkits 1.6.1CC1([C@@H](N[C@H](S1)[C@@H](C(=O)O)NC(=O)[C@@H](c2ccccc2)N)C(=O)O)C
CACTVS 3.352CC1(C)S[CH](N[CH]1C(O)=O)[CH](NC(=O)[CH](N)c2ccccc2)C(O)=O
FormulaC16 H21 N3 O5 S
Name(2R,4S)-2-[(R)-{[(2R)-2-amino-2-phenylacetyl]amino}(carboxy)methyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid;
AMPICILLIN (open form)
ChEMBLCHEMBL1237008
DrugBank
ZINCZINC000034064298
PDB chain6xd7 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6xd7 KPC-2 beta-lactamase enables carbapenem antibiotic resistance through fast deacylation of the covalent intermediate.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		C69 S70 W105 S130 N132 E166 L167 A170 T237 C238
Binding residue
(residue number reindexed from 1)		C44 S45 W80 S105 N107 E141 L142 A145 T212 C213
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S70 K73 S130 E166 K234 T237
Catalytic site (residue number reindexed from 1) S45 K48 S105 E141 K209 T212
Enzyme Commision number 3.5.2.6: beta-lactamase.
Gene Ontology
Molecular Function
GO:0008800 beta-lactamase activity
Biological Process
GO:0017001 antibiotic catabolic process
GO:0030655 beta-lactam antibiotic catabolic process
GO:0046677 response to antibiotic

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6xd7, PDBe:6xd7, PDBj:6xd7
PDBsum6xd7
PubMed33273017
UniProtQ9F663|BLKPC_KLEPN Carbapenem-hydrolyzing beta-lactamase KPC (Gene Name=bla)

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