scPDB - 4dxj entry

Protein Data Bank Entry:

PDB ID : 4dxj

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2012-02-27

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:	33.533
Number of residues:	31
Including
Standard Amino Acids:	23
Non Standard Amino Acids:	4
Water Molecules:	4
Cofactors:
Metals:	MG MG MG

Cavity properties

Ligandability	Volume (Å3)
0.352	637.875

% Hydrophobic	% Polar
44.97	55.03
According to VolSite

Ligand :

HET Code:	0M9
Formula:	C5H12NO6P2
Molecular weight:	244.099 g/mol
DrugBank ID:	-
Buried Surface Area:	66.99 %
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:	6

Mass center Coordinates

X	Y	Z
47.9356	50.5068	204.728

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
C6	CB	TYR- 94	4.13	0	Hydrophobic	false
N1	OD1	ASP- 98	3.81	0	Ionic (Ligand Cationic)	false
O1	NH1	ARG- 107	2.74	170.83	H-Bond (Protein Donor)	false
O1	NH2	ARG- 107	3.42	129.88	H-Bond (Protein Donor)	false
O2	NH2	ARG- 107	2.84	140.28	H-Bond (Protein Donor)	false
O1	CZ	ARG- 107	3.52	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 107	3.69	0	Ionic (Protein Cationic)	false
C5	CG2	THR- 163	3.75	0	Hydrophobic	false
C5	CG	GLN- 167	4.03	0	Hydrophobic	false
O4	NZ	LYS- 207	2.94	145.61	H-Bond (Protein Donor)	false
O4	NZ	LYS- 207	2.94	0	Ionic (Protein Cationic)	false
O5	NZ	LYS- 207	3.98	0	Ionic (Protein Cationic)	false
C5	CB	LYS- 207	4.27	0	Hydrophobic	false
C5	CE2	TYR- 211	3.59	0	Hydrophobic	false
O1	NZ	LYS- 264	2.61	140.15	H-Bond (Protein Donor)	false
O3	NZ	LYS- 264	3.05	127.58	H-Bond (Protein Donor)	false
O1	NZ	LYS- 264	2.61	0	Ionic (Protein Cationic)	false
O3	NZ	LYS- 264	3.05	0	Ionic (Protein Cationic)	false
O6	MG	MG- 401	1.91	0	Metal Acceptor	false
O2	MG	MG- 402	2.16	0	Metal Acceptor	false
O6	MG	MG- 402	2.19	0	Metal Acceptor	false
O3	MG	MG- 403	1.83	0	Metal Acceptor	false
O5	MG	MG- 403	2.03	0	Metal Acceptor	false