scPDB - 2f4j entry

Protein Data Bank Entry:

PDB ID : 2f4j

Resolution :1.910 Å

Experimental Method : X-ray

Deposition Date : 2005-11-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	5.140	7.660	8.020	0.880	8.520	24

List of CHEMBLId :

CHEMBL572878

Binding Site :

Uniprot Annotation

Name:	Tyrosine-protein kinase ABL1
ID:	ABL1_HUMAN
AC:	P00519
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.10.2

Chains:

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

Ligand binding site composition:

B-Factor:	20.008
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.213	448.875

% Hydrophobic	% Polar
62.41	37.59
According to VolSite

Ligand :

HET Code:	VX6
Formula:	C23H29N8OS
Molecular weight:	465.594 g/mol
DrugBank ID:	-
Buried Surface Area:	57.35 %
Polar Surface area:	128.57 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
1.99018	-7.50097	-24.5694

Binding mode :

What is Poseview ?

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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
C3	CD2	LEU- 248	4.44	0	Hydrophobic	false
C9	CD1	LEU- 248	4.38	0	Hydrophobic	false
S23	CB	LEU- 248	3.96	0	Hydrophobic	false
C29	CB	LEU- 248	4.23	0	Hydrophobic	false
S23	CD1	TYR- 253	3.77	0	Hydrophobic	false
C25	CG	TYR- 253	3.42	0	Hydrophobic	false
C25	CB	TYR- 253	3.98	0	Hydrophobic	false
C28	CG1	VAL- 256	3.55	0	Hydrophobic	false
C29	CG2	VAL- 256	3.46	0	Hydrophobic	false
C21	CB	ALA- 269	3.89	0	Hydrophobic	false
C35	CD	LYS- 271	3.91	0	Hydrophobic	false
C34	SD	MET- 290	4.04	0	Hydrophobic	false
C21	CG2	VAL- 299	4.22	0	Hydrophobic	false
C35	CG2	ILE- 313	3.82	0	Hydrophobic	false
C21	CB	THR- 315	4.21	0	Hydrophobic	false
C34	CG2	THR- 315	3.89	0	Hydrophobic	false
N19	O	GLU- 316	2.63	133.09	H-Bond (Ligand Donor)	false
N14	O	MET- 318	3.11	145.46	H-Bond (Ligand Donor)	false
N20	N	MET- 318	2.73	154.76	H-Bond (Protein Donor)	false
C21	CD1	LEU- 370	3.77	0	Hydrophobic	false
C25	CD2	LEU- 370	4.32	0	Hydrophobic	false
N30	OD1	ASP- 381	3.07	160.52	H-Bond (Ligand Donor)	false