scPDB - 4ge5 entry

Protein Data Bank Entry:

PDB ID : 4ge5

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2012-08-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Tyrosine-protein phosphatase non-receptor type 9
ID:	PTN9_HUMAN
AC:	P43378
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:	22.894
Number of residues:	31
Including
Standard Amino Acids:	30
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.137	313.875

% Hydrophobic	% Polar
35.48	64.52
According to VolSite

Ligand :

HET Code:	A89
Formula:	C30H29BrF2IN4O7P
Molecular weight:	833.353 g/mol
DrugBank ID:	-
Buried Surface Area:	38.76 %
Polar Surface area:	203.39 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	3
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
15.5862	-0.514326	-4.19815

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
I	CG	PRO- 315	4.09	0	Hydrophobic	false
C29	CB	TYR- 333	4.2	0	Hydrophobic	false
C8	CG	TYR- 333	3.59	0	Hydrophobic	false
N1	OD2	ASP- 335	3.02	141.93	H-Bond (Ligand Donor)	false
N1	OD1	ASP- 335	2.82	148.96	H-Bond (Ligand Donor)	false
N2	OD2	ASP- 335	2.69	162.23	H-Bond (Ligand Donor)	false
N4	O	ASP- 335	3.06	153.54	H-Bond (Ligand Donor)	false
C18	CB	ASP- 335	4.2	0	Hydrophobic	false
C26	CB	ASP- 335	3.98	0	Hydrophobic	false
C8	CG2	VAL- 336	3.83	0	Hydrophobic	false
C13	CG2	VAL- 336	4.44	0	Hydrophobic	false
C19	CG	PRO- 337	4.39	0	Hydrophobic	false
C7	CB	SER- 516	4.42	0	Hydrophobic	false
O2	N	ALA- 517	3.08	163.61	H-Bond (Protein Donor)	false
C4	CB	ALA- 517	3.46	0	Hydrophobic	false
C4	CD1	ILE- 519	3.87	0	Hydrophobic	false
C3	CG1	ILE- 519	3.81	0	Hydrophobic	false
C14	CD1	ILE- 519	4.11	0	Hydrophobic	false
O1	N	ILE- 519	2.99	158	H-Bond (Protein Donor)	false
O1	N	GLY- 520	2.72	165.83	H-Bond (Protein Donor)	false
O3	N	ARG- 521	2.71	173.32	H-Bond (Protein Donor)	false
F2	CB	GLN- 559	3.58	0	Hydrophobic	false
C3	CG	GLN- 559	3.54	0	Hydrophobic	false
N3	OE1	GLN- 559	2.65	135.95	H-Bond (Ligand Donor)	false