scPDB - 4g2w entry

Protein Data Bank Entry:

PDB ID : 4g2w

Resolution :2.280 Å

Experimental Method : X-ray

Deposition Date : 2012-07-13

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	cGMP-specific 3',5'-cyclic phosphodiesterase
ID:	PDE5A_HUMAN
AC:	O76074
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	36.891
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.801	540.000

% Hydrophobic	% Polar
58.75	41.25
According to VolSite

Ligand :

HET Code:	NI0
Formula:	C22H33N4O4S
Molecular weight:	449.587 g/mol
DrugBank ID:	-
Buried Surface Area:	50.47 %
Polar Surface area:	100.89 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	2
Rings:	3
Aromatic rings:	1
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
27.8174	-18.346	19.7558

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
CAM	CZ	TYR- 612	3.93	0	Hydrophobic	false
CAB	CE1	TYR- 612	3.65	0	Hydrophobic	false
CAR	CD1	LEU- 725	4.44	0	Hydrophobic	false
CAC	CB	LEU- 765	4.31	0	Hydrophobic	false
CAL	CD2	LEU- 765	4.38	0	Hydrophobic	false
CAC	CB	ALA- 767	4.2	0	Hydrophobic	false
CAC	CB	ILE- 768	4.41	0	Hydrophobic	false
CAA	CB	ALA- 779	3.98	0	Hydrophobic	false
CAA	CG1	VAL- 782	3.74	0	Hydrophobic	false
CAM	CG2	VAL- 782	4.07	0	Hydrophobic	false
CAK	CG1	VAL- 782	3.83	0	Hydrophobic	false
CAK	CB	ALA- 783	3.9	0	Hydrophobic	false
CAN	CD2	PHE- 786	3.64	0	Hydrophobic	false
CAB	CZ	PHE- 786	4.13	0	Hydrophobic	false
CAK	CE2	PHE- 787	4.35	0	Hydrophobic	false
CAA	CG2	ILE- 813	4.23	0	Hydrophobic	false
CAI	CB	MET- 816	3.87	0	Hydrophobic	false
CAA	CG	GLN- 817	4.27	0	Hydrophobic	false
NAT	OE1	GLN- 817	2.88	177.71	H-Bond (Ligand Donor)	false
OAE	NE2	GLN- 817	2.89	166.38	H-Bond (Protein Donor)	false
CAM	CE2	PHE- 820	4.49	0	Hydrophobic	false
CAC	CZ	PHE- 820	3.97	0	Hydrophobic	false
CAJ	CB	PHE- 820	3.76	0	Hydrophobic	false