scPDB - 4c8g entry

Protein Data Bank Entry:

PDB ID : 4c8g

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2013-10-01

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_BURCJ
AC:	B4EC22
Organism:	Burkholderia cenocepacia )
Reign:	Bacteria
TaxID:	216591
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	10.833
Number of residues:	27
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.709	607.500

% Hydrophobic	% Polar
50.00	50.00
According to VolSite

Ligand :

HET Code:	C5P
Formula:	C9H12N3O8P
Molecular weight:	321.181 g/mol
DrugBank ID:	DB03403
Buried Surface Area:	58.81 %
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
2.4289	25.0824	20.0655

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'	OD2	ASP- 58	3.2	144.99	H-Bond (Ligand Donor)	false
O2'	OD1	ASP- 58	2.98	155.77	H-Bond (Ligand Donor)	false
C3'	CG2	ILE- 59	4.39	0	Hydrophobic	false
O3'	N	GLY- 60	2.97	132.39	H-Bond (Protein Donor)	false
N4	O	ALA- 102	2.94	171.35	H-Bond (Ligand Donor)	false
N4	O	PRO- 105	3.05	147.81	H-Bond (Ligand Donor)	false
N3	N	LEU- 107	2.84	169.08	H-Bond (Protein Donor)	false
O2	N	LEU- 107	3.33	131.99	H-Bond (Protein Donor)	false
O2	N	ALA- 108	2.82	133.85	H-Bond (Protein Donor)	false
C2'	CB	ALA- 133	4.21	0	Hydrophobic	false
O1P	NZ	LYS- 134	3.72	0	Ionic (Protein Cationic)	false
O2P	NZ	LYS- 134	3.3	0	Ionic (Protein Cationic)	false
O2P	NZ	LYS- 134	3.3	147.17	H-Bond (Protein Donor)	false
O3P	OG1	THR- 135	3.38	126.86	H-Bond (Protein Donor)	false
O1P	N	THR- 135	2.82	143.17	H-Bond (Protein Donor)	false
O1P	OG1	THR- 135	3	171.53	H-Bond (Protein Donor)	false