scPDB - 2fjm entry

Protein Data Bank Entry:

PDB ID : 2fjm

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2006-01-03

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	30 %
B	70 %

Ligand binding site composition:

B-Factor:	42.082
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
0.482	502.875

% Hydrophobic	% Polar
51.68	48.32
According to VolSite

Ligand :

HET Code:	073
Formula:	C32H26F2N3O5P
Molecular weight:	601.537 g/mol
DrugBank ID:	-
Buried Surface Area:	69.18 %
Polar Surface area:	130.01 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	0
Rings:	5
Aromatic rings:	5
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
7.72121	43.9936	17.496

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
C67	CB	ALA- 518	3.83	0	Hydrophobic	false
C67	CG1	ILE- 519	4.34	0	Hydrophobic	false
C60	CB	GLN- 521	4.24	0	Hydrophobic	false
C67	CB	ASP- 522	4.16	0	Hydrophobic	false
C21	CB	ASP- 522	4.47	0	Hydrophobic	false
C59	CB	ASP- 522	3.99	0	Hydrophobic	false
C21	CB	HIS- 525	3.69	0	Hydrophobic	false
C16	CG	GLU- 526	4.03	0	Hydrophobic	false
C13	CG	TYR- 546	3.55	0	Hydrophobic	false
C17	CB	ARG- 547	4.37	0	Hydrophobic	false
N22	N	ASP- 548	3.03	151.6	H-Bond (Protein Donor)	false
C49	CB	ASP- 548	3.83	0	Hydrophobic	false
C3	CG2	VAL- 549	3.81	0	Hydrophobic	false
C49	CG2	VAL- 549	3.63	0	Hydrophobic	false
F29	CB	ASP- 681	3.52	0	Hydrophobic	false
C28	CZ	PHE- 682	3.93	0	Hydrophobic	false
F30	CE1	PHE- 682	3.48	0	Hydrophobic	false
F29	CE2	PHE- 682	3.54	0	Hydrophobic	false
O34	N	SER- 716	3.03	129.28	H-Bond (Protein Donor)	false
O34	N	ALA- 717	2.92	171.49	H-Bond (Protein Donor)	false
C4	CB	ALA- 717	3.49	0	Hydrophobic	false
C3	CD1	ILE- 719	3.91	0	Hydrophobic	false
C4	CG1	ILE- 719	3.75	0	Hydrophobic	false
C45	CD1	ILE- 719	3.62	0	Hydrophobic	false
O33	N	ILE- 719	3.16	156.55	H-Bond (Protein Donor)	false
O33	N	GLY- 720	2.87	171.04	H-Bond (Protein Donor)	false
O34	CZ	ARG- 721	3.76	0	Ionic (Protein Cationic)	false
O32	CZ	ARG- 721	3.72	0	Ionic (Protein Cationic)	false
O34	NH2	ARG- 721	2.81	162.1	H-Bond (Protein Donor)	false
O32	NE	ARG- 721	2.94	166.09	H-Bond (Protein Donor)	false
O32	N	ARG- 721	2.92	165.12	H-Bond (Protein Donor)	false
C48	SD	MET- 758	3.56	0	Hydrophobic	false
C4	CG	GLN- 762	4.09	0	Hydrophobic	false
F30	CG	GLN- 762	3.53	0	Hydrophobic	false
O32	O	HOH- 804	2.63	179.97	H-Bond (Protein Donor)	false