scPDB - 3cs9 entry

Protein Data Bank Entry:

PDB ID : 3cs9

Resolution :2.210 Å

Experimental Method : X-ray

Deposition Date : 2008-04-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.180	7.740	7.850	0.500	8.440	15

List of CHEMBLId :

CHEMBL255863

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	95 %
B	5 %

Ligand binding site composition:

B-Factor:	37.964
Number of residues:	42
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.959	1525.500

% Hydrophobic	% Polar
42.26	57.74
According to VolSite

Ligand :

HET Code:	NIL
Formula:	C28H22F3N7O
Molecular weight:	529.516 g/mol
DrugBank ID:	DB04868
Buried Surface Area:	72.5 %
Polar Surface area:	97.62 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	2
Rings:	5
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
28.0859	2.50208	52.0705

Binding mode :

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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
C36	CD1	LEU- 248	4.36	0	Hydrophobic	false
C41	CD1	LEU- 248	3.62	0	Hydrophobic	false
C36	CB	TYR- 253	4.26	0	Hydrophobic	false
C27	CG1	VAL- 256	4.16	0	Hydrophobic	false
C36	CG1	VAL- 256	4.27	0	Hydrophobic	false
C27	CB	ALA- 269	3.97	0	Hydrophobic	false
C41	CB	ALA- 269	4.47	0	Hydrophobic	false
C25	CD	LYS- 271	4.4	0	Hydrophobic	false
C27	CB	LYS- 271	3.78	0	Hydrophobic	false
C58	CG	LYS- 285	3.83	0	Hydrophobic	false
N14	OE2	GLU- 286	2.99	134.44	H-Bond (Ligand Donor)	false
C9	CG	GLU- 286	3.88	0	Hydrophobic	false
C58	CG2	VAL- 289	3.86	0	Hydrophobic	false
C9	CG	MET- 290	4.03	0	Hydrophobic	false
C12	CE	MET- 290	4.27	0	Hydrophobic	false
C18	CE	MET- 290	3.96	0	Hydrophobic	false
C25	SD	MET- 290	3.77	0	Hydrophobic	false
F3	CD1	ILE- 293	3.38	0	Hydrophobic	false
F4	CD2	LEU- 298	3.8	0	Hydrophobic	false
F3	CD2	LEU- 298	4.34	0	Hydrophobic	false
C12	CG1	VAL- 299	4.3	0	Hydrophobic	false
F4	CG1	VAL- 299	4.2	0	Hydrophobic	false
C19	CG1	VAL- 299	4.29	0	Hydrophobic	false
C23	CG2	ILE- 313	3.83	0	Hydrophobic	false
N31	OG1	THR- 315	2.92	138.53	H-Bond (Ligand Donor)	false
C22	CG2	THR- 315	3.32	0	Hydrophobic	false
N44	N	MET- 318	2.98	154.81	H-Bond (Protein Donor)	false
F3	CD1	LEU- 354	4.42	0	Hydrophobic	false
F3	CE1	PHE- 359	3.92	0	Hydrophobic	false
C41	CD2	LEU- 370	3.92	0	Hydrophobic	false
F1	CG1	VAL- 379	3.8	0	Hydrophobic	false
O17	N	ASP- 381	3.08	166.78	H-Bond (Protein Donor)	false
F1	CB	ASP- 381	3.81	0	Hydrophobic	false
C5	CB	ASP- 381	3.61	0	Hydrophobic	false