scPDB - 3qpo entry

Protein Data Bank Entry:

PDB ID : 3qpo

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2011-02-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A
ID:	PDE10_RAT
AC:	Q9QYJ6
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	3.1.4.17

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	25.462
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.008	712.125

% Hydrophobic	% Polar
56.87	43.13
According to VolSite

Ligand :

HET Code:	PFR
Formula:	C27H28N4O2
Molecular weight:	440.537 g/mol
DrugBank ID:	-
Buried Surface Area:	47.58 %
Polar Surface area:	60.37 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	5
Aromatic rings:	4
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
11.5371	19.5608	40.7962

Binding mode :

What is Poseview ?

2D View
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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
C15	CD2	LEU- 625	4.45	0	Hydrophobic	false
C19	CD2	LEU- 625	4.04	0	Hydrophobic	false
C13	CG1	VAL- 668	3.78	0	Hydrophobic	false
C13	CD1	ILE- 682	3.8	0	Hydrophobic	false
C4	CG2	ILE- 682	4.21	0	Hydrophobic	false
C26	CZ	TYR- 683	4	0	Hydrophobic	false
N29	OH	TYR- 683	2.76	166.49	H-Bond (Protein Donor)	false
C26	CE2	PHE- 686	4.12	0	Hydrophobic	false
C3	SD	MET- 703	4.03	0	Hydrophobic	false
C16	CE	MET- 703	3.67	0	Hydrophobic	false
C18	SD	MET- 703	3.85	0	Hydrophobic	false
C26	SD	MET- 703	3.96	0	Hydrophobic	false
C32	CB	MET- 703	3.61	0	Hydrophobic	false
O11	NE2	GLN- 716	3.38	165.44	H-Bond (Protein Donor)	false
C2	CB	PHE- 719	4.3	0	Hydrophobic	false
C13	CE2	PHE- 719	3.74	0	Hydrophobic	false
C19	CD1	PHE- 719	3.96	0	Hydrophobic	false
C27	CB	PHE- 719	4.03	0	Hydrophobic	false
C22	CB	PHE- 719	4.09	0	Hydrophobic	false
DuAr	DuAr	PHE- 719	3.82	0	Aromatic Face/Face	false
C23	CB	ALA- 722	3.96	0	Hydrophobic	false
C24	CG2	VAL- 723	3.6	0	Hydrophobic	false