scPDB - 3t80 entry

Protein Data Bank Entry:

PDB ID : 3t80

Resolution :2.500 Å

Experimental Method : X-ray

Deposition Date : 2011-07-31

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_SALTY
AC:	Q8ZMF7
Organism:	Salmonella typhimurium
Reign:	Bacteria
TaxID:	99287
EC Number:	4.6.1.12

Chains:

Chain Name:	Percentage of Residues within binding site
A	35 %
C	65 %

Ligand binding site composition:

B-Factor:	51.033
Number of residues:	24
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.097	735.750

% Hydrophobic	% Polar
52.29	47.71
According to VolSite

Ligand :

HET Code:	CTN
Formula:	C9H13N3O5
Molecular weight:	243.217 g/mol
DrugBank ID:	DB02097
Buried Surface Area:	56.93 %
Polar Surface area:	128.61 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	4
Rings:	2
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-10.0552	20.1897	2.79018

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
O2'	OD2	ASP- 56	3.48	157.62	H-Bond (Ligand Donor)	false
N4	O	ALA- 100	2.66	174.57	H-Bond (Ligand Donor)	false
N4	O	PRO- 103	3.22	168.63	H-Bond (Ligand Donor)	false
N3	N	MET- 105	2.97	165.39	H-Bond (Protein Donor)	false
O2	N	MET- 105	3.09	132.82	H-Bond (Protein Donor)	false
C1'	CB	LEU- 106	4.39	0	Hydrophobic	false
O2	N	LEU- 106	2.89	144.53	H-Bond (Protein Donor)	false
C2'	CB	ALA- 131	3.98	0	Hydrophobic	false