scPDB - 3k3e entry

Protein Data Bank Entry:

PDB ID : 3k3e

Resolution :2.700 Å

Experimental Method : X-ray

Deposition Date : 2009-10-02

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
ID:	PDE9A_HUMAN
AC:	O76083
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:	47.183
Number of residues:	30
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	2
Water Molecules:	0
Cofactors:
Metals:	ZN MG

Cavity properties

Ligandability	Volume (Å3)
1.149	823.500

% Hydrophobic	% Polar
52.46	47.54
According to VolSite

Ligand :

HET Code:	PDB
Formula:	C15H12ClF3N4O
Molecular weight:	356.730 g/mol
DrugBank ID:	-
Buried Surface Area:	56.01 %
Polar Surface area:	59.28 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
97.051	21.8997	10.3742

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
C3	CG	MET- 365	3.85	0	Hydrophobic	false
CL1	CG2	ILE- 403	3.92	0	Hydrophobic	false
F5	CG1	VAL- 417	4.21	0	Hydrophobic	false
C5	CD1	LEU- 420	4.04	0	Hydrophobic	false
C6	CD2	LEU- 420	3.68	0	Hydrophobic	false
F5	CD2	LEU- 420	3.38	0	Hydrophobic	false
F7	CG	LEU- 421	3.61	0	Hydrophobic	false
F7	CE2	TYR- 424	4.27	0	Hydrophobic	false
C20	CE2	TYR- 424	3.83	0	Hydrophobic	false
C20	CD1	PHE- 441	3.83	0	Hydrophobic	false
C20	CB	ALA- 452	4.41	0	Hydrophobic	false
C21	CB	ALA- 452	4.44	0	Hydrophobic	false
F6	CG	GLN- 453	4.23	0	Hydrophobic	false
N15	OE1	GLN- 453	2.56	171.51	H-Bond (Ligand Donor)	false
O17	NE2	GLN- 453	2.81	167.24	H-Bond (Protein Donor)	false
C18	CG	PHE- 456	4.27	0	Hydrophobic	false
CL1	CE1	PHE- 456	3.32	0	Hydrophobic	false