scPDB - 3n8y entry

Protein Data Bank Entry:

PDB ID : 3n8y

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2010-05-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Prostaglandin G/H synthase 1
ID:	PGH1_SHEEP
AC:	P05979
Organism:	Ovis aries
Reign:	Eukaryota
TaxID:	9940
EC Number:	1.14.99.1

Chains:

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

Ligand binding site composition:

B-Factor:	39.032
Number of residues:	30
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.640	816.750

% Hydrophobic	% Polar
68.18	31.82
According to VolSite

Ligand :

HET Code:	DIF
Formula:	C14H10Cl2NO2
Molecular weight:	295.141 g/mol
DrugBank ID:	DB00586
Buried Surface Area:	72.22 %
Polar Surface area:	52.16 Å2

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

Mass center Coordinates

X	Y	Z
33.3644	-45.3042	-3.40305

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
C13	CE2	TYR- 348	3.73	0	Hydrophobic	false
CL4	CG1	VAL- 349	4.14	0	Hydrophobic	false
C13	CG2	VAL- 349	4.29	0	Hydrophobic	false
C3	CG1	VAL- 349	3.42	0	Hydrophobic	false
CL2	CG	LEU- 352	3.6	0	Hydrophobic	false
C13	CD2	LEU- 352	3.82	0	Hydrophobic	false
C7	CD1	LEU- 352	3.82	0	Hydrophobic	false
CL2	CB	SER- 353	3.68	0	Hydrophobic	false
C1	CB	SER- 353	3.69	0	Hydrophobic	false
C11	CD2	LEU- 384	4.12	0	Hydrophobic	false
C13	CZ	TYR- 385	4.42	0	Hydrophobic	false
O1	OH	TYR- 385	2.68	161.06	H-Bond (Protein Donor)	false
C13	CH2	TRP- 387	4.19	0	Hydrophobic	false
CL2	CZ	PHE- 518	4.41	0	Hydrophobic	false
C1	CG2	ILE- 523	3.9	0	Hydrophobic	false
CL2	CD1	ILE- 523	3.39	0	Hydrophobic	false
CL4	CB	ALA- 527	4.04	0	Hydrophobic	false
C9	CB	ALA- 527	4.04	0	Hydrophobic	false
C5	CB	ALA- 527	3.55	0	Hydrophobic	false
CL4	CB	SER- 530	3.62	0	Hydrophobic	false
O2	OG	SER- 530	2.53	156.96	H-Bond (Protein Donor)	false
CL4	CG	LEU- 531	3.63	0	Hydrophobic	false
C5	CD1	LEU- 531	4.42	0	Hydrophobic	false