scPDB - 2vd0 entry

Protein Data Bank Entry:

PDB ID : 2vd0

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2007-09-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Hematopoietic prostaglandin D synthase
ID:	HPGDS_HUMAN
AC:	O60760
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:	20.429
Number of residues:	21
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.684	702.000

% Hydrophobic	% Polar
49.52	50.48
According to VolSite

Ligand :

HET Code:	D27
Formula:	C18H16NO5
Molecular weight:	326.323 g/mol
DrugBank ID:	DB07615
Buried Surface Area:	58.36 %
Polar Surface area:	87.69 Å2

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

Mass center Coordinates

X	Y	Z
128.244	14.2938	-1.04888

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
C16	SD	MET- 11	3.61	0	Hydrophobic	false
C7	CE	MET- 11	4.07	0	Hydrophobic	false
O15	CZ	ARG- 14	3.63	0	Ionic (Protein Cationic)	false
O15	NH1	ARG- 14	2.54	150.26	H-Bond (Protein Donor)	false
C1	CG	ARG- 14	3.62	0	Hydrophobic	false
C23	CG	MET- 99	3.81	0	Hydrophobic	false
C18	CB	MET- 99	3.45	0	Hydrophobic	false
C24	CE	MET- 99	3.8	0	Hydrophobic	false
C21	CB	TRP- 104	3.87	0	Hydrophobic	false
C10	CB	TRP- 104	3.5	0	Hydrophobic	false
C21	CB	ALA- 105	3.85	0	Hydrophobic	false
C24	CG2	ILE- 155	4.3	0	Hydrophobic	false
C23	SG	CYS- 156	3.65	0	Hydrophobic	false
C16	CD1	LEU- 199	3.7	0	Hydrophobic	false