scPDB - 4jvb entry

Protein Data Bank Entry:

PDB ID : 4jvb

Resolution :1.750 Å

Experimental Method : X-ray

Deposition Date : 2013-03-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
ID:	PDE6D_HUMAN
AC:	O43924
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	30.584
Number of residues:	44
Including
Standard Amino Acids:	43
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.094	820.125

% Hydrophobic	% Polar
70.78	29.22
According to VolSite

Ligand :

HET Code:	1M0
Formula:	C38H32N4O
Molecular weight:	560.687 g/mol
DrugBank ID:	-
Buried Surface Area:	72.13 %
Polar Surface area:	44.87 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	0
Rings:	7
Aromatic rings:	7
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
21.9831	-5.94293	-14.5191

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
CBE	CD1	LEU- 17	3.69	0	Hydrophobic	false
CBD	SD	MET- 20	3.82	0	Hydrophobic	false
CBO	CE	MET- 20	3.72	0	Hydrophobic	false
CBF	CE	MET- 20	4.04	0	Hydrophobic	false
CBN	CD1	LEU- 22	3.92	0	Hydrophobic	false
CAU	CD2	LEU- 22	3.78	0	Hydrophobic	false
CAN	CD1	LEU- 22	3.58	0	Hydrophobic	false
CBF	CB	LEU- 38	3.98	0	Hydrophobic	false
CBN	CD1	LEU- 38	3.81	0	Hydrophobic	false
CBL	CB	ALA- 47	3.65	0	Hydrophobic	false
CBM	CG1	VAL- 49	4.43	0	Hydrophobic	false
CAN	CG1	VAL- 49	3.78	0	Hydrophobic	false
CAO	CG2	VAL- 49	3.64	0	Hydrophobic	false
CAP	CG2	ILE- 53	3.26	0	Hydrophobic	false
CAO	CD1	ILE- 53	3.49	0	Hydrophobic	false
CAE	CD2	LEU- 54	4.36	0	Hydrophobic	false
CAC	CD2	LEU- 54	3.97	0	Hydrophobic	false
CBJ	CG2	VAL- 59	4.41	0	Hydrophobic	false
CBQ	CG2	VAL- 59	3.94	0	Hydrophobic	false
CBD	CD	ARG- 61	4.36	0	Hydrophobic	false
NAZ	NH1	ARG- 61	2.92	143.17	H-Bond (Protein Donor)	false
CBD	CD1	LEU- 63	3.85	0	Hydrophobic	false
NAZ	NE2	GLN- 78	3.03	164.68	H-Bond (Protein Donor)	false
CAA	CG1	VAL- 80	4.29	0	Hydrophobic	false
CAB	CG2	VAL- 80	3.8	0	Hydrophobic	false
CAQ	CZ2	TRP- 90	4.2	0	Hydrophobic	false
CAQ	CG2	ILE- 109	3.79	0	Hydrophobic	false
CBQ	CG2	ILE- 109	4.44	0	Hydrophobic	false
CAT	CD1	ILE- 109	3.7	0	Hydrophobic	false
CBQ	CB	ALA- 111	3.79	0	Hydrophobic	false
CAB	SD	MET- 117	3.49	0	Hydrophobic	false
CAC	CG1	VAL- 127	4.44	0	Hydrophobic	false
CBK	CD1	ILE- 129	4.48	0	Hydrophobic	false
CBH	CG2	ILE- 129	3.86	0	Hydrophobic	false
CAW	CG2	ILE- 129	3.91	0	Hydrophobic	false
CAX	CD1	ILE- 129	3.96	0	Hydrophobic	false
CAL	CD1	ILE- 129	3.32	0	Hydrophobic	false
CBE	CG2	THR- 131	4.4	0	Hydrophobic	false
CBH	CG2	VAL- 145	4.5	0	Hydrophobic	false
CBG	CG2	VAL- 145	4.45	0	Hydrophobic	false
CBK	CG1	VAL- 145	3.97	0	Hydrophobic	false
CBK	CD1	LEU- 147	4.18	0	Hydrophobic	false
CAL	CD2	LEU- 147	3.33	0	Hydrophobic	false
NAG	OH	TYR- 149	2.61	158.73	H-Bond (Protein Donor)	false