scPDB - 4a9m entry

Protein Data Bank Entry:

PDB ID : 4a9m

Resolution :2.060 Å

Experimental Method : X-ray

Deposition Date : 2011-11-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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	24 %
C	76 %

Ligand binding site composition:

B-Factor:	41.242
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.572	823.500

% Hydrophobic	% Polar
57.79	42.21
According to VolSite

Ligand :

HET Code:	P9M
Formula:	C17H22N2O3S
Molecular weight:	334.433 g/mol
DrugBank ID:	-
Buried Surface Area:	55.67 %
Polar Surface area:	80.58 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
1.88504	7.03109	21.3066

Binding mode :

What is Poseview ?

2D View
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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
C17	CB	ASN- 77	3.67	0	Hydrophobic	false
C10	CZ3	TRP- 97	4.42	0	Hydrophobic	false
C14	CH2	TRP- 97	3.59	0	Hydrophobic	false
C15	CG	PRO- 98	3.81	0	Hydrophobic	false
C14	CB	PRO- 98	3.91	0	Hydrophobic	false
C8	CB	PRO- 98	3.79	0	Hydrophobic	false
C1	CE1	PHE- 99	3.31	0	Hydrophobic	false
C1	CG2	VAL- 103	4.36	0	Hydrophobic	false
C7	CG2	VAL- 103	4.1	0	Hydrophobic	false
C10	CD2	LEU- 108	3.59	0	Hydrophobic	false
C9	CD1	LEU- 108	3.65	0	Hydrophobic	false
C4	CD1	LEU- 110	3.56	0	Hydrophobic	false
C4	CE1	TYR- 113	3.94	0	Hydrophobic	false
C1	SG	CYS- 152	4.33	0	Hydrophobic	false
C4	CD2	TYR- 155	3.62	0	Hydrophobic	false
O1	ND2	ASN- 156	2.92	164.13	H-Bond (Protein Donor)	false
N1	ND2	ASN- 156	3.36	150.27	H-Bond (Protein Donor)	false
C16	CB	ASP- 161	4.44	0	Hydrophobic	false
C6	CD1	ILE- 162	4.36	0	Hydrophobic	false
C1	CD1	ILE- 162	3.89	0	Hydrophobic	false
C15	CD1	ILE- 162	3.98	0	Hydrophobic	false
C15	SD	MET- 165	3.77	0	Hydrophobic	false