scPDB - 4gfv entry

Protein Data Bank Entry:

PDB ID : 4gfv

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2012-08-04

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 18
ID:	PTN18_HUMAN
AC:	Q99952
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:	21.319
Number of residues:	27
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.308	567.000

% Hydrophobic	% Polar
39.88	60.12
According to VolSite

Ligand :

HET Code:	PRO_GLU_LEU_THR_PTR
Formula:	C29H42N5O12P
Molecular weight:	683.644 g/mol
DrugBank ID:	-
Buried Surface Area:	37.72 %
Polar Surface area:	292.66 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	6
Rings:	2
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
36.1647	-29.4188	4.62619

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
CG	CD1	TYR- 62	4.29	0	Hydrophobic	false
CB	CG	TYR- 62	3.58	0	Hydrophobic	false
N	OD2	ASP- 64	3.33	122.16	H-Bond (Ligand Donor)	false
N	OD1	ASP- 64	2.82	170.79	H-Bond (Ligand Donor)	false
N	OD2	ASP- 64	2.94	155.3	H-Bond (Ligand Donor)	false
CG	CB	ASP- 64	4.17	0	Hydrophobic	false
CD1	CG2	VAL- 65	3.77	0	Hydrophobic	false
CD2	CG2	VAL- 65	4.35	0	Hydrophobic	false
CB	CG2	VAL- 65	3.73	0	Hydrophobic	false
O	NH2	ARG- 198	2.99	146.82	H-Bond (Protein Donor)	false
O	NH1	ARG- 198	3.36	155.34	H-Bond (Protein Donor)	false
O2P	OG	SER- 229	2.79	148.97	H-Bond (Protein Donor)	false
O3P	OG	SER- 229	3.38	143.44	H-Bond (Protein Donor)	false
CE1	CB	SER- 230	4.46	0	Hydrophobic	false
O1P	N	SER- 230	2.94	140.44	H-Bond (Protein Donor)	false
O1P	N	ALA- 231	3.14	166.77	H-Bond (Protein Donor)	false
CG	CB	ALA- 231	3.57	0	Hydrophobic	false
CD2	SG	CYS- 233	4.33	0	Hydrophobic	false
CE2	CB	CYS- 233	4.16	0	Hydrophobic	false
O2P	N	CYS- 233	2.62	156.72	H-Bond (Protein Donor)	false
O2P	N	GLY- 234	3.08	120.74	H-Bond (Protein Donor)	false
O1P	CZ	ARG- 235	3.65	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 235	3.65	0	Ionic (Protein Cationic)	false
O1P	NH2	ARG- 235	2.8	172.89	H-Bond (Protein Donor)	false
O3P	N	ARG- 235	2.94	168.65	H-Bond (Protein Donor)	false
O3P	NE	ARG- 235	2.79	170.41	H-Bond (Protein Donor)	false
O3P	O	HOH- 401	2.96	169.13	H-Bond (Protein Donor)	false