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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:

2yel

1.650 Å

X-ray

2011-03-25

Activity from ChEMBL: What is pChEMBL ?
MinMeanMedianStandard DeviationMaxCount
pChEMBL:7.2807.5407.6200.1907.7203

List of CHEMBLId :

CHEMBL1738926


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:17.823
Number of residues:21
Including
Standard Amino Acids: 20
Non Standard Amino Acids: 0
Water Molecules: 1
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.218340.875

% Hydrophobic% Polar
68.3231.68
According to VolSite

Ligand :
2yel_1 Structure
HET Code: WSH
Formula: C25H21N5O2
Molecular weight: 423.467 g/mol
DrugBank ID: -
Buried Surface Area:46.39 %
Polar Surface area: 81.4 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 1
Rings: 5
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 5

Mass center Coordinates

XYZ
-11.1192-7.110592.39844


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
C1CBPRO- 824.10Hydrophobic
C19CGPRO- 823.850Hydrophobic
C24CBPRO- 823.860Hydrophobic
C1CE1PHE- 833.750Hydrophobic
C24CG2VAL- 874.340Hydrophobic
C1CG2VAL- 873.990Hydrophobic
C21CD2LEU- 924.110Hydrophobic
C12CBLEU- 924.210Hydrophobic
C10CD2LEU- 923.660Hydrophobic
C23CD1LEU- 923.560Hydrophobic
C6CD2LEU- 943.670Hydrophobic
N2ND2ASN- 1402.99160.54H-Bond
(Protein Donor)
N3OD1ASN- 1402.94137.08H-Bond
(Ligand Donor)
C17CBASP- 1453.970Hydrophobic
C1CD1ILE- 1464.040Hydrophobic
C19CD1ILE- 1463.450Hydrophobic
C14CBILE- 1463.780Hydrophobic
C25CD1ILE- 1464.120Hydrophobic
C18SDMET- 1493.630Hydrophobic