Structure of PDB 5ctn Chain B Binding Site BS01

Receptor Information
>5ctn Chain B (length=232) Species: 1408 (Bacillus pumilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SIAWSVDEFFKNREGTFVIQEVKEKSPWVYNKKRAKERFAPQSTFKVANA
LIGLQTGAVRDEYDIKYWDGVKREIDNWNRDHTLGSGMRDSVVWYYQAMA
RDIGEERMNHWVKAIHYGNKDISGGIDQFWLSSTLRISPIEQVRFLKQLY
EETLPFDLKNMRTVKRMMVQEEEKHATLYGKTGSGSDIGWYVGFIKHEHK
TYILATNIKGTGIEAKDITYRILKKYHLMEAS
Ligand information
Ligand ID5R7
InChIInChI=1S/C15H26N4O6S2/c1-7-12(11(6-20)8(2)21)19-13(15(22)23)14(7)26-10-3-9(17-5-10)4-18-27(16,24)25/h6-12,14,17-18,21H,3-5H2,1-2H3,(H,22,23)(H2,16,24,25)/t7-,8-,9+,10+,11-,12-,14-/m1/s1
InChIKeyRBKUPZPTQNSPAV-QZOCKBNKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6C[C@H]1[C@H](C(=N[C@H]1[C@H](C=O)[C@@H](C)O)C(=O)O)S[C@H]2C[C@H](NC2)CNS(=O)(=O)N
ACDLabs 12.01CC(O)C(C=O)C2N=C(C(O)=O)C(SC1CNC(CNS(N)(=O)=O)C1)C2C
CACTVS 3.385C[C@@H](O)[C@@H](C=O)[C@@H]1N=C([C@H](S[C@@H]2CN[C@H](CN[S](N)(=O)=O)C2)[C@@H]1C)C(O)=O
CACTVS 3.385C[CH](O)[CH](C=O)[CH]1N=C([CH](S[CH]2CN[CH](CN[S](N)(=O)=O)C2)[CH]1C)C(O)=O
OpenEye OEToolkits 1.7.6CC1C(C(=NC1C(C=O)C(C)O)C(=O)O)SC2CC(NC2)CNS(=O)(=O)N
FormulaC15 H26 N4 O6 S2
Name(2~{S},3~{R})-3-methyl-2-[(2~{S},3~{R})-3-oxidanyl-1-oxidanylidene-butan-2-yl]-4-[(3~{S},5~{S})-5-[(sulfamoylamino)meth yl]pyrrolidin-3-yl]sulfanyl-3,4-dihydro-2~{H}-pyrrole-5-carboxylic acid;
Doripenem(open form, pyrroline tautomer form 3, SP3 connection to Thio as R isomer)
ChEMBL
DrugBank
ZINCZINC000263620964
PDB chain5ctn Chain B Residue 300 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ctn Class D beta-lactamases do exist in Gram-positive bacteria.
Resolution1.35 Å
Binding residue
(original residue number in PDB)
Q100 S101 W136 S149 V151 L189 G241 S242
Binding residue
(residue number reindexed from 1)
Q42 S43 W78 S91 V93 L131 G183 S184
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) S101 K104 S149 Y154 W188 S242
Catalytic site (residue number reindexed from 1) S43 K46 S91 Y96 W130 S184
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
Biological Process
GO:0017001 antibiotic catabolic process
GO:0046677 response to antibiotic
GO:0071555 cell wall organization

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Molecular Function

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Biological Process
External links
PDB RCSB:5ctn, PDBe:5ctn, PDBj:5ctn
PDBsum5ctn
PubMed26551395
UniProtA8FFI9

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