Structure of PDB 4mjp Chain B Binding Site BS01

Receptor Information
>4mjp Chain B (length=359) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKFTVEREHLLKPLQQVSGPPILGNLLLQVADGTLSLTGTDLEMEMVARV
ALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFS
LSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNG
MLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGVIELMRML
DGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPKNPDKHLE
AGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQEEAEEILD
VTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSA
AYVVMPMRL
Ligand information
Ligand ID27O
InChIInChI=1S/C19H22O2/c1-13(19(20)21)15-11-12-16(14-7-3-2-4-8-14)18-10-6-5-9-17(15)18/h5-6,9-14H,2-4,7-8H2,1H3,(H,20,21)/t13-/m1/s1
InChIKeyVZUGVMQFWFVFBX-CYBMUJFWSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@@H](C(O)=O)c1ccc(C2CCCCC2)c3ccccc13
OpenEye OEToolkits 1.7.6C[C@H](c1ccc(c2c1cccc2)C3CCCCC3)C(=O)O
ACDLabs 12.01O=C(O)C(c2ccc(c1ccccc12)C3CCCCC3)C
OpenEye OEToolkits 1.7.6CC(c1ccc(c2c1cccc2)C3CCCCC3)C(=O)O
CACTVS 3.385C[CH](C(O)=O)c1ccc(C2CCCCC2)c3ccccc13
FormulaC19 H22 O2
Name(2R)-2-(4-cyclohexylnaphthalen-1-yl)propanoic acid;
(R)-Vedaprofen
ChEMBLCHEMBL1966247
DrugBank
ZINCZINC000001842638
PDB chain4mjp Chain B Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4mjp DNA replication is the target for the antibacterial effects of nonsteroidal anti-inflammatory drugs.
Resolution1.855 Å
Binding residue
(original residue number in PDB)		T172 R240 P242 D243 R246 V247
Binding residue
(residue number reindexed from 1)		T165 R233 P235 D236 R239 V240
Annotation score1
Binding affinityMOAD: Ki=131uM
PDBbind-CN: -logKd/Ki=3.88,Ki=131uM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4mjp, PDBe:4mjp, PDBj:4mjp
PDBsum4mjp
PubMed24631121
UniProtP0A988|DPO3B_ECOLI Beta sliding clamp (Gene Name=dnaN)

[Back to BioLiP]