scPDB - 3svg entry

Protein Data Bank Entry:

PDB ID : 3svg

Resolution :1.680 Å

Experimental Method : X-ray

Deposition Date : 2011-07-12

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 4
ID:	BRD4_HUMAN
AC:	O60885
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	13.588
Number of residues:	19
Including
Standard Amino Acids:	17
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.947	246.375

% Hydrophobic	% Polar
71.23	28.77
According to VolSite

Ligand :

HET Code:	ODR
Formula:	C15H19NO3
Molecular weight:	261.316 g/mol
DrugBank ID:	-
Buried Surface Area:	47.63 %
Polar Surface area:	55.49 Å2

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

Mass center Coordinates

X	Y	Z
29.7309	16.172	-1.65579

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
CAA	CZ3	TRP- 81	4.32	0	Hydrophobic	false
CAS	CH2	TRP- 81	4.36	0	Hydrophobic	false
CAB	CB	PRO- 82	4.07	0	Hydrophobic	false
CAL	CB	PRO- 82	4	0	Hydrophobic	false
CAS	CG	PRO- 82	4.44	0	Hydrophobic	false
CAD	CB	PRO- 82	3.65	0	Hydrophobic	false
CAL	CE1	PHE- 83	4.3	0	Hydrophobic	false
CAL	CG2	VAL- 87	3.94	0	Hydrophobic	false
CAB	CD1	LEU- 92	4.07	0	Hydrophobic	false
CAD	CD2	LEU- 92	4.31	0	Hydrophobic	false
CAI	CD1	LEU- 92	3.84	0	Hydrophobic	false
CAP	CD1	LEU- 94	3.83	0	Hydrophobic	false
OAN	ND2	ASN- 140	3.21	162.99	H-Bond (Protein Donor)	false
CAS	CB	ASP- 145	4.14	0	Hydrophobic	false
CAL	CD1	ILE- 146	3.72	0	Hydrophobic	false
CAS	CD1	ILE- 146	4.04	0	Hydrophobic	false
CAG	CD1	ILE- 146	3.65	0	Hydrophobic	false
CAS	SD	MET- 149	3.55	0	Hydrophobic	false