scPDB - 4dwb entry

Protein Data Bank Entry:

PDB ID : 4dwb

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2012-02-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Farnesyl pyrophosphate synthase
ID:	Q95WL3_TRYCR
AC:	Q95WL3
Organism:	Trypanosoma cruzi
Reign:	Eukaryota
TaxID:	5693
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	28.706
Number of residues:	30
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	4
Water Molecules:	3
Cofactors:
Metals:	MG MG MG

Cavity properties

Ligandability	Volume (Å3)
0.128	698.625

% Hydrophobic	% Polar
41.06	58.94
According to VolSite

Ligand :

HET Code:	0M7
Formula:	C7H16NO6P2
Molecular weight:	272.153 g/mol
DrugBank ID:	-
Buried Surface Area:	66.78 %
Polar Surface area:	162.61 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	1
Rings:	0
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
12.1424	16.9641	176.142

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
C10	CG	TYR- 94	3.53	0	Hydrophobic	false
C9	CB	TYR- 94	3.51	0	Hydrophobic	false
C8	CB	ASP- 98	4.03	0	Hydrophobic	false
O13	CZ	ARG- 107	3.82	0	Ionic (Protein Cationic)	false
O12	CZ	ARG- 107	3.34	0	Ionic (Protein Cationic)	false
O13	NH2	ARG- 107	2.72	145.26	H-Bond (Protein Donor)	false
O12	NH1	ARG- 107	2.68	159.95	H-Bond (Protein Donor)	false
O12	NH2	ARG- 107	3.11	134.14	H-Bond (Protein Donor)	false
C10	CG2	THR- 163	3.48	0	Hydrophobic	false
O16	NZ	LYS- 207	2.83	145.62	H-Bond (Protein Donor)	false
O16	NZ	LYS- 207	2.83	0	Ionic (Protein Cationic)	false
C10	CE2	TYR- 211	3.33	0	Hydrophobic	false
O11	NZ	LYS- 264	2.6	146.02	H-Bond (Protein Donor)	false
O12	NZ	LYS- 264	2.83	132.01	H-Bond (Protein Donor)	false
O11	NZ	LYS- 264	2.6	0	Ionic (Protein Cationic)	false
O12	NZ	LYS- 264	2.83	0	Ionic (Protein Cationic)	false
O14	MG	MG- 506	2.47	0	Metal Acceptor	false
O13	MG	MG- 507	2.09	0	Metal Acceptor	false
O14	MG	MG- 507	1.97	0	Metal Acceptor	false
O11	MG	MG- 508	2.1	0	Metal Acceptor	false
O15	MG	MG- 508	1.82	0	Metal Acceptor	false