scPDB - 3jvh entry

Protein Data Bank Entry:

PDB ID : 3jvh

Resolution :1.690 Å

Experimental Method : X-ray

Deposition Date : 2009-09-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
ID:	ISPF_BURP1
AC:	Q3JRA0
Organism:	Burkholderia pseudomallei
Reign:	Bacteria
TaxID:	320372
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	77 %
B	23 %

Ligand binding site composition:

B-Factor:	12.785
Number of residues:	29
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.586	806.625

% Hydrophobic	% Polar
46.86	53.14
According to VolSite

Ligand :

HET Code:	HHV
Formula:	C10H11N5O
Molecular weight:	217.227 g/mol
DrugBank ID:	-
Buried Surface Area:	52.99 %
Polar Surface area:	96.69 Å2

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

Mass center Coordinates

X	Y	Z
8.65856	-28.6867	-18.6608

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
N04	OD2	ASP- 48	2.95	171.24	H-Bond (Ligand Donor)	false
N16	OD2	ASP- 58	3.38	162.84	H-Bond (Ligand Donor)	false
C07	CG2	ILE- 59	4.02	0	Hydrophobic	false
C07	CB	ASP- 65	4.29	0	Hydrophobic	false
C13	CB	ASP- 65	4.48	0	Hydrophobic	false
DuAr	NZ	LYS- 134	3.43	163.54	Pi/Cation	false
N10	ZN	ZN- 163	2	0	Metal Acceptor	false
DuAr	ZN	ZN- 163	3.34	82.68	Pi/Cation	false