scPDB - 2yek entry

Protein Data Bank Entry:

PDB ID : 2yek

Resolution :1.980 Å

Experimental Method : X-ray

Deposition Date : 2011-03-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.640	7.070	7.100	0.240	7.340	8

List of CHEMBLId :

CHEMBL1232461

Binding Site :

Uniprot Annotation

Name:	Bromodomain-containing protein 2
ID:	BRD2_HUMAN
AC:	P25440
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	28 %
C	72 %

Ligand binding site composition:

B-Factor:	32.996
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.093	982.125

% Hydrophobic	% Polar
53.61	46.39
According to VolSite

Ligand :

HET Code:	EAM
Formula:	C22H22ClN5O2
Molecular weight:	423.895 g/mol
DrugBank ID:	-
Buried Surface Area:	60.77 %
Polar Surface area:	81.4 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
2.14923	6.71067	20.2225

Binding mode :

What is Poseview ?

2D View
3D View

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

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
CL	CB	ASN- 77	3.78	0	Hydrophobic	false
C11	CB	ASN- 77	4.25	0	Hydrophobic	false
O2	NE2	GLN- 80	3.03	151.43	H-Bond (Protein Donor)	false
C14	CG	GLN- 80	4.32	0	Hydrophobic	false
C16	CG	LYS- 84	3.74	0	Hydrophobic	false
CL	CZ2	TRP- 97	4.04	0	Hydrophobic	false
C16	CE3	TRP- 97	4.26	0	Hydrophobic	false
C9	CH2	TRP- 97	3.43	0	Hydrophobic	false
C21	CB	PRO- 98	4.37	0	Hydrophobic	false
C8	CG	PRO- 98	3.72	0	Hydrophobic	false
C17	CB	PRO- 98	4.02	0	Hydrophobic	false
C21	CE1	PHE- 99	3.97	0	Hydrophobic	false
C18	CG2	VAL- 103	4.1	0	Hydrophobic	false
C21	CG2	VAL- 103	3.56	0	Hydrophobic	false
C14	CD2	LEU- 108	4.07	0	Hydrophobic	false
C18	CD1	LEU- 108	3.8	0	Hydrophobic	false
C4	CD1	LEU- 110	3.94	0	Hydrophobic	false
C1	CD2	LEU- 110	4.24	0	Hydrophobic	false
C4	CE2	TYR- 155	4.05	0	Hydrophobic	false
N5	ND2	ASN- 156	3.16	164.85	H-Bond (Protein Donor)	false
CL	CB	ASP- 161	3.68	0	Hydrophobic	false
C9	CB	ILE- 162	4.13	0	Hydrophobic	false
C21	CD1	ILE- 162	3.64	0	Hydrophobic	false
C8	CD1	ILE- 162	3.51	0	Hydrophobic	false
C19	CD1	ILE- 162	3.8	0	Hydrophobic	false
CL	SD	MET- 165	4.27	0	Hydrophobic	false
C9	SD	MET- 165	3.87	0	Hydrophobic	false
CL	CG	PRO- 181	3.69	0	Hydrophobic	false
C11	CD2	LEU- 187	4.24	0	Hydrophobic	false
C12	CD1	LEU- 187	4.01	0	Hydrophobic	false