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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

4j3i

1.240 Å

X-ray

2013-02-05

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:5.0506.2006.2400.6306.8506

List of CHEMBLId :

CHEMBL2393130


Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Bromodomain-containing protein 4
ID:BRD4_HUMAN
AC:O60885
Organism:Homo sapiens
Reign:Eukaryota
TaxID:9606
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:6.909
Number of residues:23
Including
Standard Amino Acids: 21
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors:
Metals: NA

Cavity properties

LigandabilityVolume (Å3)
1.145317.250

% Hydrophobic% Polar
69.1530.85
According to VolSite

Ligand :
4j3i_1 Structure
HET Code: 1K0
Formula: C20H22N2O5
Molecular weight: 370.399 g/mol
DrugBank ID: DB12000
Buried Surface Area:37.5 %
Polar Surface area: 89.38 Å2
Number of
H-Bond Acceptors: 6
H-Bond Donors: 2
Rings: 3
Aromatic rings: 2
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 6

Mass center Coordinates

XYZ
-13.0119-7.25973.04919


Binding mode :
What is Poseview ?
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C1CZ3TRP- 813.780Hydrophobic
C1CBPRO- 824.210Hydrophobic
C3CBPRO- 823.710Hydrophobic
C5CE1PHE- 833.540Hydrophobic
C5CG2VAL- 873.70Hydrophobic
C4CG2VAL- 873.810Hydrophobic
C1CD1LEU- 924.020Hydrophobic
C20CD1LEU- 923.580Hydrophobic
C9CD1LEU- 944.390Hydrophobic
C10CD2LEU- 943.90Hydrophobic
N1OD1ASN- 1402.91152.03H-Bond
(Ligand Donor)
O5ND2ASN- 1402.85163.2H-Bond
(Protein Donor)
C17CBASP- 1444.130Hydrophobic
C5CD1ILE- 1464.160Hydrophobic
C6CG1ILE- 1463.740Hydrophobic
C18CG2ILE- 1464.20Hydrophobic
C4CD1ILE- 1463.660Hydrophobic