Structure of PDB 3d4f Chain A Binding Site BS02

Receptor Information
>3d4f Chain A (length=265) Species: 573 (Klebsiella pneumoniae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SPQPLEQIKLSESQLSGRVGMIEMDLASGRTLTAWRADERFPMMSTFKVV
LCGAVLARVDAGDEQLERKIHYRQQDLVDYSPVSEKHLADGMTVGELCAA
AITMSDNSAANLLLATVGGPAGLTAFLRQIGDNVTRLDRWETELNEALPG
DARDTTTPASMAATLRKLLTSQRLSARSQRQLLQWMVDDRVAGPLIRSVL
PAGWFIADKTGAGERGARGIVALLGPNNKAERIVVIYLRDTPASMAERNQ
QIAGIGAALIEHWQR
Ligand information
Ligand IDLN1
InChIInChI=1S/C22H22N2O9S/c1-22(34(31)32,12-33-18(28)9-13-5-6-16(26)17(27)8-13)19(21(29)30)23-20-14(11-25)10-15-4-2-3-7-24(15)20/h2-8,10-11,19,23,26-27H,9,12H2,1H3,(H,29,30)(H,31,32)/t19-,22-/m0/s1
InChIKeyDEOZLEGRVHDNKC-UGKGYDQZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341C[C](COC(=O)Cc1ccc(O)c(O)c1)([CH](Nc2n3ccccc3cc2C=O)C(O)=O)[S](O)=O
OpenEye OEToolkits 1.5.0C[C@](COC(=O)Cc1ccc(c(c1)O)O)([C@H](C(=O)O)Nc2c(cc3n2cccc3)C=O)[S@@](=O)O
ACDLabs 10.04O=C(OCC(S(=O)O)(C)C(C(=O)O)Nc2c(cc1ccccn12)C=O)Cc3ccc(O)c(O)c3
OpenEye OEToolkits 1.5.0CC(COC(=O)Cc1ccc(c(c1)O)O)(C(C(=O)O)Nc2c(cc3n2cccc3)C=O)S(=O)O
CACTVS 3.341C[C@](COC(=O)Cc1ccc(O)c(O)c1)([C@@H](Nc2n3ccccc3cc2C=O)C(O)=O)[S@](O)=O
FormulaC22 H22 N2 O9 S
Name(3R)-4-{[(3,4-dihydroxyphenyl)acetyl]oxy}-N-(2-formylindolizin-3-yl)-3-sulfino-D-valine
ChEMBL
DrugBankDB08116
ZINCZINC000058639150
PDB chain3d4f Chain A Residue 601 [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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PDB3d4f Strategic Design of an Effective {beta}-Lactamase Inhibitor: LN-1-255, A 6-ALKYLIDENE-2'-SUBSTITUTED PENICILLIN SULFONE
Resolution1.55 Å
Binding residue
(original residue number in PDB)		S70 S130 V216 L220 T235 G236 A237 R244 N276
Binding residue
(residue number reindexed from 1)		S45 S105 V191 L195 T210 G211 A212 R218 N249
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.72,Kd=19nM
Enzymatic activity
Catalytic site (original residue number in PDB) S70 K73 S130 E166 K234 A237
Catalytic site (residue number reindexed from 1) S45 K48 S105 E141 K209 A212
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:3d4f, PDBe:3d4f, PDBj:3d4f
PDBsum3d4f
PubMed18955486
UniProtP0AD64|BLA1_KLEPN Beta-lactamase SHV-1 (Gene Name=bla)

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