Structure of PDB 3qsb Chain A Binding Site BS01

Receptor Information
>3qsb Chain A (length=366) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLE
MEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVR
SGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQD
VRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGV
IELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPK
NPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQE
EAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIE
DAASQSAAYVVMPMRL
Ligand information
Ligand ID743
InChIInChI=1S/C26H27FN2O3/c1-4-5-22(24-23(30)14-26(2,3)21(15-28)25(24)31)29-32-16-17-6-8-18(9-7-17)19-10-12-20(27)13-11-19/h6-13,21,24H,4-5,14,16H2,1-3H3/b29-22-/t21-,24-/m1/s1
InChIKeyQRVDHQOKZPXAJH-FQRCLESUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCCC(=NOCc1ccc(cc1)c2ccc(cc2)F)C3C(=O)CC(C(C3=O)C#N)(C)C
OpenEye OEToolkits 1.7.0CCC/C(=N/OCc1ccc(cc1)c2ccc(cc2)F)/[C@@H]3C(=O)CC([C@@H](C3=O)C#N)(C)C
CACTVS 3.370CCCC(=NOCc1ccc(cc1)c2ccc(F)cc2)[CH]3C(=O)CC(C)(C)[CH](C#N)C3=O
ACDLabs 12.01Fc1ccc(cc1)c2ccc(cc2)CO\N=C(/C3C(=O)CC(C)(C)C(C#N)C3=O)CCC
CACTVS 3.370CCCC(=N/OCc1ccc(cc1)c2ccc(F)cc2)/[C@@H]3C(=O)CC(C)(C)[C@H](C#N)C3=O
FormulaC26 H27 F N2 O3
Name(1R,5R)-5-{(1Z)-N-[(4'-fluorobiphenyl-4-yl)methoxy]butanimidoyl}-2,2-dimethyl-4,6-dioxocyclohexanecarbonitrile
ChEMBL
DrugBank
ZINCZINC000103529428
PDB chain3qsb Chain A Residue 367 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3qsb Binding inhibitors of the bacterial sliding clamp by design
Resolution1.9 Å
Binding residue
(original residue number in PDB)		T172 G174 V247 V360 M362
Binding residue
(residue number reindexed from 1)		T172 G174 V247 V360 M362
Annotation score1
Binding affinityMOAD: ic50=8.3uM
PDBbind-CN: -logKd/Ki=5.08,IC50=8.3uM
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0005515 protein binding
GO:0008408 3'-5' exonuclease activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006271 DNA strand elongation involved in DNA replication
GO:0006974 DNA damage response
GO:0030174 regulation of DNA-templated DNA replication initiation
GO:0032297 negative regulation of DNA-templated DNA replication initiation
GO:0042276 error-prone translesion synthesis
GO:0044787 bacterial-type DNA replication
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0009360 DNA polymerase III complex
GO:0030894 replisome
GO:1990078 replication inhibiting complex
GO:1990085 Hda-beta clamp complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3qsb, PDBe:3qsb, PDBj:3qsb
PDBsum3qsb
PubMed21604761
UniProtP0A988|DPO3B_ECOLI Beta sliding clamp (Gene Name=dnaN)

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