scPDB - 1h47 entry

Protein Data Bank Entry:

PDB ID : 1h47

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2003-02-24

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_ECOLI
AC:	P62617
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	4.6.1.12

Chains:

Chain Name:	Percentage of Residues within binding site
D	39 %
E	61 %

Ligand binding site composition:

B-Factor:	34.545
Number of residues:	29
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.322	735.750

% Hydrophobic	% Polar
35.32	64.68
According to VolSite

Ligand :

HET Code:	C5P
Formula:	C9H12N3O8P
Molecular weight:	321.181 g/mol
DrugBank ID:	DB03403
Buried Surface Area:	57.98 %
Polar Surface area:	190.61 Å2

Number of
H-Bond Acceptors:	10
H-Bond Donors:	3
Rings:	2
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
34.5532	36.0861	26.1183

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
O2'	OD1	ASP- 56	2.91	143.09	H-Bond (Ligand Donor)	false
O2'	OD2	ASP- 56	3.11	156.9	H-Bond (Ligand Donor)	false
O3'	N	GLY- 58	3.12	128.58	H-Bond (Protein Donor)	false
N4	O	ALA- 100	2.97	174.34	H-Bond (Ligand Donor)	false
N4	O	PRO- 103	3.01	151.22	H-Bond (Ligand Donor)	false
O4'	NZ	LYS- 104	3.46	137.7	H-Bond (Protein Donor)	false
N3	N	MET- 105	3.08	160.67	H-Bond (Protein Donor)	false
O2	N	MET- 105	3.39	140.57	H-Bond (Protein Donor)	false
O2	N	LEU- 106	2.97	143.74	H-Bond (Protein Donor)	false
O3P	OG1	THR- 133	2.61	158.38	H-Bond (Protein Donor)	false
O3P	N	THR- 133	2.91	141.45	H-Bond (Protein Donor)	false
O3'	O	HOH- 2005	2.93	164.44	H-Bond (Ligand Donor)	false