scPDB - 3prf entry

Protein Data Bank Entry:

PDB ID : 3prf

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2010-11-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serine/threonine-protein kinase B-raf
ID:	BRAF_HUMAN
AC:	P15056
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.11.1

Chains:

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

Ligand binding site composition:

B-Factor:	56.217
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.887	604.125

% Hydrophobic	% Polar
46.37	53.63
According to VolSite

Ligand :

HET Code:	FP3
Formula:	C17H11ClN4O2
Molecular weight:	338.748 g/mol
DrugBank ID:	-
Buried Surface Area:	64.57 %
Polar Surface area:	84.07 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	4
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	3

Mass center Coordinates

X	Y	Z
82.4955	7.3915	-7.83325

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
C3	CG1	VAL- 471	3.77	0	Hydrophobic	false
C4	CG2	VAL- 471	3.91	0	Hydrophobic	false
C3	CB	ALA- 481	3.83	0	Hydrophobic	false
C13	CB	ALA- 481	3.54	0	Hydrophobic	false
C6	CD	LYS- 483	4.12	0	Hydrophobic	false
C1	CB	LYS- 483	3.96	0	Hydrophobic	false
O23	NZ	LYS- 483	3.08	138.51	H-Bond (Protein Donor)	false
O23	OE2	GLU- 501	3.26	152.64	H-Bond (Ligand Donor)	false
C13	CD1	LEU- 514	4.05	0	Hydrophobic	false
C1	CD2	LEU- 514	4.18	0	Hydrophobic	false
CL1	CG2	ILE- 527	3.59	0	Hydrophobic	false
CL1	CG2	THR- 529	3.67	0	Hydrophobic	false
N9	N	CYS- 532	2.88	157.29	H-Bond (Protein Donor)	false