Structure of PDB 6dmh Chain A Binding Site BS01

Receptor Information
>6dmh Chain A (length=270) Species: 47917 (Serratia fonticola) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASQPPQVTVDKLKRLENDFGGRIGVYAIDTGSNKTFGYRANERFPLCSSF
KGFLAAAVLSKSQQQEGLLNQRIRYDNRVMEPHSPVTEKQITTGMTVAEL
SAATLQYSDNGAANLLLEKLIGGPEGMTSFMRSIGDNVFRLDRWALELNS
AIPGDDRDTSTPKAVAESMQKLAFGNVLGLTERHQLMDWFKGNTTGGARI
RASVPANWVVGDKTGTCGVYGTANDYAVIWPVAHAPIVLAVYTSKPDRNS
KHSDAVIADASRIVLESFNI
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 chain6dmh Chain A Residue 305 [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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PDB6dmh qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps.
Resolution1.3 Å
Binding residue
(original residue number in PDB)		S70 S130 N170 T235 G236 T237
Binding residue
(residue number reindexed from 1)		S48 S108 N149 T214 G215 T216
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S70 K73 S130 A166 K234 T237
Catalytic site (residue number reindexed from 1) S48 K51 S108 A145 K213 T216
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:6dmh, PDBe:6dmh, PDBj:6dmh
PDBsum6dmh
PubMed30457858
UniProtQ6JP75

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