scPDB - 3k14 entry

Protein Data Bank Entry:

PDB ID : 3k14

Resolution :1.700 Å

Experimental Method : X-ray

Deposition Date : 2009-09-25

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	88 %
B	12 %

Ligand binding site composition:

B-Factor:	20.220
Number of residues:	28
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.907	705.375

% Hydrophobic	% Polar
52.15	47.85
According to VolSite

Ligand :

HET Code:	535
Formula:	C9H10N2O2S
Molecular weight:	210.253 g/mol
DrugBank ID:	-
Buried Surface Area:	63.87 %
Polar Surface area:	71.84 Å2

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

Mass center Coordinates

X	Y	Z
6.49407	-27.6314	-16.6786

Binding mode :

What is Poseview ?

2D View
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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	CB	HIS- 36	4.32	0	Hydrophobic	false
C13	CB	SER- 37	4.14	0	Hydrophobic	false
S8	CD1	ILE- 59	4.1	0	Hydrophobic	false
C12	CB	PHE- 63	4.33	0	Hydrophobic	false
C13	CB	ASP- 65	4.1	0	Hydrophobic	false
C13	CB	PHE- 70	4.26	0	Hydrophobic	false
C12	CD1	LEU- 78	3.91	0	Hydrophobic	false
N1	ZN	ZN- 163	1.93	0	Metal Acceptor	false