scPDB - 1jf7 entry

Protein Data Bank Entry:

PDB ID : 1jf7

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2001-06-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	5.700	5.700	5.700	0.000	5.700	2

List of CHEMBLId :

CHEMBL299120

Binding Site :

Uniprot Annotation

Name:	Tyrosine-protein phosphatase non-receptor type 1
ID:	PTN1_HUMAN
AC:	P18031
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.1.3.48

Chains:

Chain Name:	Percentage of Residues within binding site
A	19 %
B	81 %

Ligand binding site composition:

B-Factor:	32.014
Number of residues:	33
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.612	1836.000

% Hydrophobic	% Polar
38.05	61.95
According to VolSite

Ligand :

HET Code:	TBH
Formula:	C31H46N3O9
Molecular weight:	604.712 g/mol
DrugBank ID:	DB02977
Buried Surface Area:	50.62 %
Polar Surface area:	200.07 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	6
Rings:	2
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	21

Mass center Coordinates

X	Y	Z
19.1938	11.5927	42.1145

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
C7	CG	TYR- 46	3.75	0	Hydrophobic	false
C39	CD1	TYR- 46	4.15	0	Hydrophobic	false
O36	N	ARG- 47	3.01	156.91	H-Bond (Protein Donor)	false
C40	CG	ARG- 47	4.41	0	Hydrophobic	false
C31	CD	ARG- 47	3.54	0	Hydrophobic	false
N13	OD2	ASP- 48	3.04	133.39	H-Bond (Ligand Donor)	false
N10	OD2	ASP- 48	2.89	138.05	H-Bond (Ligand Donor)	false
N10	OD1	ASP- 48	2.8	153.24	H-Bond (Ligand Donor)	false
C30	CB	ASP- 48	3.86	0	Hydrophobic	false
C7	CG2	VAL- 49	4.01	0	Hydrophobic	false
O43	NZ	LYS- 120	3.23	0	Ionic (Protein Cationic)	false
O42	NZ	LYS- 120	3.11	0	Ionic (Protein Cationic)	false
O42	NZ	LYS- 120	3.11	156.8	H-Bond (Protein Donor)	false
C23	CZ	PHE- 182	3.81	0	Hydrophobic	false
C16	CZ	PHE- 182	4.47	0	Hydrophobic	false
O25	N	PHE- 182	3.1	143.66	H-Bond (Protein Donor)	false
C2	CB	ALA- 217	3.35	0	Hydrophobic	false
C2	CG1	ILE- 219	3.76	0	Hydrophobic	false
C3	CD1	ILE- 219	3.88	0	Hydrophobic	false
O25	N	ARG- 221	3.47	125.66	H-Bond (Protein Donor)	false
O26	N	ARG- 221	3.05	173.28	H-Bond (Protein Donor)	false
O26	NE	ARG- 221	3.13	161.5	H-Bond (Protein Donor)	false
C23	CG	GLN- 262	4.06	0	Hydrophobic	false
C2	CG	GLN- 262	4.09	0	Hydrophobic	false
O25	NE2	GLN- 266	2.95	151.14	H-Bond (Protein Donor)	false
C28	CZ	PHE- 280	4.09	0	Hydrophobic	false