scPDB - 4jvf entry

Protein Data Bank Entry:

PDB ID : 4jvf

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2013-03-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	10.110	10.110	10.110	0.000	10.110	1

List of CHEMBLId :

CHEMBL3286930

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:	31.822
Number of residues:	42
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.784	847.125

% Hydrophobic	% Polar
62.15	37.85
According to VolSite

Ligand :

HET Code:	17X
Formula:	C40H43N6O2
Molecular weight:	639.808 g/mol
DrugBank ID:	-
Buried Surface Area:	72.65 %
Polar Surface area:	81.79 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	1
Rings:	8
Aromatic rings:	6
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
-34.41	5.13888	-4.66102

Binding mode :

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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
CAX	CD1	LEU- 17	3.91	0	Hydrophobic	false
CAC	SD	MET- 20	4.4	0	Hydrophobic	false
CAI	CE	MET- 20	3.88	0	Hydrophobic	false
CAE	CE	MET- 20	4.07	0	Hydrophobic	false
CAW	SD	MET- 20	3.93	0	Hydrophobic	false
CAR	CD1	LEU- 22	4.21	0	Hydrophobic	false
CAK	CD1	LEU- 22	3.91	0	Hydrophobic	false
CBA	CD1	LEU- 22	4.09	0	Hydrophobic	false
CAJ	CD1	LEU- 38	3.64	0	Hydrophobic	false
CAE	CB	LEU- 38	4.09	0	Hydrophobic	false
CAK	CB	ALA- 47	3.65	0	Hydrophobic	false
CBB	CG2	VAL- 49	4.25	0	Hydrophobic	false
CAL	CG1	VAL- 49	4.29	0	Hydrophobic	false
CBE	CG1	ILE- 53	4.49	0	Hydrophobic	false
CBB	CG2	ILE- 53	3.92	0	Hydrophobic	false
CAZ	CD1	ILE- 53	3.72	0	Hydrophobic	false
CBN	CD2	LEU- 54	3.58	0	Hydrophobic	false
NBV	O	CYS- 56	2.58	129.01	H-Bond (Ligand Donor)	false
CAZ	CG1	VAL- 59	4.48	0	Hydrophobic	false
CAW	CD	ARG- 61	4.47	0	Hydrophobic	false
NAY	NH1	ARG- 61	2.94	121.43	H-Bond (Protein Donor)	false
CAW	CD2	LEU- 63	4.24	0	Hydrophobic	false
NAY	NE2	GLN- 78	2.92	149.9	H-Bond (Protein Donor)	false
CBK	CG1	VAL- 80	3.65	0	Hydrophobic	false
CBL	CD2	LEU- 87	4.37	0	Hydrophobic	false
CBP	CZ2	TRP- 90	4.31	0	Hydrophobic	false
CBU	CZ2	TRP- 90	4.12	0	Hydrophobic	false
CAN	CD1	ILE- 109	4.16	0	Hydrophobic	false
CAP	CD1	ILE- 109	4.45	0	Hydrophobic	false
CBP	CG2	ILE- 109	3.67	0	Hydrophobic	false
CBU	CG2	ILE- 109	4.2	0	Hydrophobic	false
CBL	CD1	LEU- 123	4.19	0	Hydrophobic	false
CBJ	CG1	VAL- 127	4.29	0	Hydrophobic	false
CBK	CG2	VAL- 127	4.25	0	Hydrophobic	false
CAM	CG1	ILE- 129	4.34	0	Hydrophobic	false
CAG	CG2	ILE- 129	3.97	0	Hydrophobic	false
CAQ	CD1	ILE- 129	4.36	0	Hydrophobic	false
CAO	CG2	ILE- 129	4.22	0	Hydrophobic	false
CAF	CG2	VAL- 145	4.34	0	Hydrophobic	false
CAM	CG1	VAL- 145	4.17	0	Hydrophobic	false
CAG	CG2	VAL- 145	4.33	0	Hydrophobic	false
CBB	CD1	LEU- 147	4.1	0	Hydrophobic	false
CAL	CD2	LEU- 147	3.36	0	Hydrophobic	false
NBF	OH	TYR- 149	2.79	170.46	H-Bond (Protein Donor)	false