scPDB - 3qcj entry

Protein Data Bank Entry:

PDB ID : 3qcj

Resolution :2.260 Å

Experimental Method : X-ray

Deposition Date : 2011-01-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Receptor-type tyrosine-protein phosphatase gamma
ID:	PTPRG_HUMAN
AC:	P23470
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.1.3.48

Chains:

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

Ligand binding site composition:

B-Factor:	38.982
Number of residues:	34
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.410	421.875

% Hydrophobic	% Polar
71.20	28.80
According to VolSite

Ligand :

HET Code:	NX4
Formula:	C20H14Cl2NO6S3
Molecular weight:	531.429 g/mol
DrugBank ID:	-
Buried Surface Area:	63.56 %
Polar Surface area:	174.52 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	3
Aromatic rings:	3
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
22.2749	30.3639	60.4186

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
CL12	CG2	ILE- 950	3.86	0	Hydrophobic	false
CL13	CD1	ILE- 950	4.22	0	Hydrophobic	false
C9	CG2	ILE- 950	3.68	0	Hydrophobic	false
C8	CB	TYR- 1023	4.43	0	Hydrophobic	false
CL12	CG	TYR- 1023	3.99	0	Hydrophobic	false
S4	CZ3	TRP- 1026	3.9	0	Hydrophobic	false
C7	CH2	TRP- 1026	3.37	0	Hydrophobic	false
S21	CB	VAL- 1031	3.69	0	Hydrophobic	false
S4	CG	PRO- 1032	4	0	Hydrophobic	false
C5	CB	PRO- 1032	4	0	Hydrophobic	false
CL13	CG1	VAL- 1038	3.89	0	Hydrophobic	false
C7	CG2	VAL- 1038	3.58	0	Hydrophobic	false
C9	CG1	VAL- 1038	3.6	0	Hydrophobic	false
C10	CG1	VAL- 1038	3.51	0	Hydrophobic	false
CL12	CD2	PHE- 1041	3.32	0	Hydrophobic	false
S4	CG	ARG- 1066	3.98	0	Hydrophobic	false
O14	NE	ARG- 1066	3.01	157.54	H-Bond (Protein Donor)	false
O17	NE	ARG- 1066	3.48	126.51	H-Bond (Protein Donor)	false
O17	NH2	ARG- 1066	2.64	161.61	H-Bond (Protein Donor)	false
O32	N	ARG- 1066	3.08	137.49	H-Bond (Protein Donor)	false
C11	CG2	THR- 1069	3.91	0	Hydrophobic	false
CL13	CG2	THR- 1069	4.26	0	Hydrophobic	false
CL13	CB	TYR- 1070	3.55	0	Hydrophobic	false
CL13	CD1	ILE- 1073	4.32	0	Hydrophobic	false
C25	CG	GLN- 1104	4.2	0	Hydrophobic	false
C29	CG	GLN- 1104	3.46	0	Hydrophobic	false
O31	NE2	GLN- 1104	2.98	146.29	H-Bond (Protein Donor)	false
C24	CG2	THR- 1105	3.69	0	Hydrophobic	false
S21	CB	GLU- 1107	3.68	0	Hydrophobic	false
O14	NE2	GLN- 1108	3.31	165.4	H-Bond (Protein Donor)	false
O32	NE2	GLN- 1108	3.24	156.75	H-Bond (Protein Donor)	false
S21	CG	GLN- 1108	3.9	0	Hydrophobic	false
C5	CE2	PHE- 1111	3.7	0	Hydrophobic	false