scPDB - 2b07 entry

Protein Data Bank Entry:

PDB ID : 2b07

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2005-09-13

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 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	100 %

Ligand binding site composition:

B-Factor:	46.324
Number of residues:	37
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.320	246.375

% Hydrophobic	% Polar
54.79	45.21
According to VolSite

Ligand :

HET Code:	598
Formula:	C25H22N2O7S3
Molecular weight:	558.646 g/mol
DrugBank ID:	-
Buried Surface Area:	52.41 %
Polar Surface area:	203.76 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	1
Rings:	5
Aromatic rings:	4
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
47.5359	9.70792	2.43241

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
C50	CB	ASP- 48	3.84	0	Hydrophobic	false
C23	CB	ASP- 48	4.37	0	Hydrophobic	false
C30	CG2	VAL- 49	3.94	0	Hydrophobic	false
C21	CG2	VAL- 49	3.63	0	Hydrophobic	false
O7	NZ	LYS- 120	3.07	155.86	H-Bond (Protein Donor)	false
O8	NZ	LYS- 120	2.67	132	H-Bond (Protein Donor)	false
O7	NZ	LYS- 120	3.07	0	Ionic (Protein Cationic)	false
O8	NZ	LYS- 120	2.67	0	Ionic (Protein Cationic)	false
C10	CE1	PHE- 182	3.7	0	Hydrophobic	false
S18	CE1	PHE- 182	4.03	0	Hydrophobic	false
O15	N	PHE- 182	2.8	141.79	H-Bond (Protein Donor)	false
S18	CB	ALA- 217	4.05	0	Hydrophobic	false
C21	CD1	ILE- 219	3.83	0	Hydrophobic	false
S18	CD1	ILE- 219	3.7	0	Hydrophobic	false
C30	CD1	ILE- 219	4.02	0	Hydrophobic	false
O14	N	ARG- 221	3.22	172.83	H-Bond (Protein Donor)	false
O14	NE	ARG- 221	3.23	150.54	H-Bond (Protein Donor)	false
C45	SD	MET- 258	4.25	0	Hydrophobic	false
C49	SD	MET- 258	4.36	0	Hydrophobic	false
C31	SD	MET- 258	4.08	0	Hydrophobic	false
S18	CG	GLN- 262	3.4	0	Hydrophobic	false
O15	NE2	GLN- 266	2.92	154.11	H-Bond (Protein Donor)	false
O14	O	HOH- 323	2.82	171.97	H-Bond (Protein Donor)	false