scPDB - 2vcz entry

Protein Data Bank Entry:

PDB ID : 2vcz

Resolution :1.950 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:	16.630
Number of residues:	20
Including
Standard Amino Acids:	19
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.491	587.250

% Hydrophobic	% Polar
52.30	47.70
According to VolSite

Ligand :

HET Code:	VC3
Formula:	C9H7N3O2
Molecular weight:	189.171 g/mol
DrugBank ID:	DB08695
Buried Surface Area:	66.37 %
Polar Surface area:	74.5 Å2

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

Mass center Coordinates

X	Y	Z
76.9049	65.8729	2.62793

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
C13	CG	ARG- 14	3.71	0	Hydrophobic	false
C11	CB	TRP- 104	4.11	0	Hydrophobic	false
DuAr	DuAr	TRP- 104	3.66	0	Aromatic Face/Face	false
N4	OH	TYR- 152	2.96	133.91	H-Bond (Ligand Donor)	false