scPDB - 1q6s entry

Protein Data Bank Entry:

PDB ID : 1q6s

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2003-08-13

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	78 %
B	22 %

Ligand binding site composition:

B-Factor:	19.368
Number of residues:	55
Including
Standard Amino Acids:	51
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.085	1528.875

% Hydrophobic	% Polar
44.37	55.63
According to VolSite

Ligand :

HET Code:	214
Formula:	C38H28F2N4O6P2
Molecular weight:	736.596 g/mol
DrugBank ID:	-
Buried Surface Area:	65.44 %
Polar Surface area:	189.6 Å2

Number of
H-Bond Acceptors:	9
H-Bond Donors:	0
Rings:	7
Aromatic rings:	7
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
37.5737	44.4998	50.7265

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
O80	NH1	ARG- 524	2.71	121.97	H-Bond (Protein Donor)	false
O82	NH1	ARG- 524	3.43	171.25	H-Bond (Protein Donor)	false
O80	CZ	ARG- 524	3.93	0	Ionic (Protein Cationic)	false
C71	CB	ASP- 529	4.23	0	Hydrophobic	false
C35	CG	TYR- 546	3.66	0	Hydrophobic	false
C3	CE1	TYR- 546	3.46	0	Hydrophobic	false
C41	CB	ARG- 547	4.29	0	Hydrophobic	false
N46	N	ASP- 548	3.11	161.85	H-Bond (Protein Donor)	false
C25	CB	ASP- 548	3.67	0	Hydrophobic	false
C35	CG2	VAL- 549	3.7	0	Hydrophobic	false
C20	CG2	VAL- 549	4.23	0	Hydrophobic	false
F53	CB	ASP- 681	3.45	0	Hydrophobic	false
F54	CZ	PHE- 682	3.67	0	Hydrophobic	false
F53	CE2	PHE- 682	3.53	0	Hydrophobic	false
O57	N	SER- 716	2.94	134.73	H-Bond (Protein Donor)	false
C35	CB	ALA- 717	4.31	0	Hydrophobic	false
C10	CB	ALA- 717	3.39	0	Hydrophobic	false
O57	N	ALA- 717	2.78	171.92	H-Bond (Protein Donor)	false
C10	CD1	ILE- 719	3.8	0	Hydrophobic	false
C15	CG1	ILE- 719	3.83	0	Hydrophobic	false
C23	CD1	ILE- 719	3.96	0	Hydrophobic	false
O56	N	ILE- 719	3.02	155.14	H-Bond (Protein Donor)	false
O56	N	GLY- 720	2.57	156.06	H-Bond (Protein Donor)	false
O57	CZ	ARG- 721	3.94	0	Ionic (Protein Cationic)	false
O58	CZ	ARG- 721	3.55	0	Ionic (Protein Cationic)	false
O57	NH2	ARG- 721	3.06	171.03	H-Bond (Protein Donor)	false
O58	N	ARG- 721	2.92	173.04	H-Bond (Protein Donor)	false
O58	NE	ARG- 721	2.75	163.8	H-Bond (Protein Donor)	false
O58	NH2	ARG- 721	3.5	127.66	H-Bond (Protein Donor)	false
O82	CZ	ARG- 754	3.83	0	Ionic (Protein Cationic)	false
O82	NH1	ARG- 754	2.91	154.55	H-Bond (Protein Donor)	false
C64	SD	MET- 758	3.55	0	Hydrophobic	false
C63	CE	MET- 758	3.32	0	Hydrophobic	false
C15	CG	GLN- 762	3.73	0	Hydrophobic	false
F54	CG	GLN- 762	3.26	0	Hydrophobic	false
C6	CB	ALA- 1017	4.18	0	Hydrophobic	false
C44	CB	ALA- 1018	4.16	0	Hydrophobic	false
C1	CB	ALA- 1018	3.65	0	Hydrophobic	false
C44	CG	GLN- 1021	3.57	0	Hydrophobic	false
C20	CG	GLN- 1021	3.76	0	Hydrophobic	false
C45	CG	GLN- 1021	3.62	0	Hydrophobic	false
O58	O	HOH- 3027	2.81	179.97	H-Bond (Protein Donor)	false
O80	O	HOH- 3110	2.69	179.95	H-Bond (Protein Donor)	false