scPDB - 3dyh entry

Protein Data Bank Entry:

PDB ID : 3dyh

Resolution :1.940 Å

Experimental Method : X-ray

Deposition Date : 2008-07-27

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:	Q86C09_9TRYP
AC:	Q86C09
Organism:	Trypanosoma brucei
Reign:	Eukaryota
TaxID:	5691
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	5 %
B	95 %

Ligand binding site composition:

B-Factor:	33.645
Number of residues:	40
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	3
Water Molecules:	3
Cofactors:
Metals:	MG MG MG

Cavity properties

Ligandability	Volume (Å3)
0.128	597.375

% Hydrophobic	% Polar
40.68	59.32
According to VolSite

Ligand :

HET Code:	721
Formula:	C11H16NO7P2
Molecular weight:	336.195 g/mol
DrugBank ID:	-
Buried Surface Area:	71.59 %
Polar Surface area:	159.1 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	0
Rings:	1
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
25.0128	-42.8413	16.2312

Binding mode :

What is Poseview ?

2D View
3D View

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- 99	4.43	0	Hydrophobic	false
C8	CG	TYR- 99	3.84	0	Hydrophobic	false
C10	CD1	TYR- 99	3.45	0	Hydrophobic	false
C6	CB	ASP- 103	4.42	0	Hydrophobic	false
O3	NH1	ARG- 112	3.1	146.59	H-Bond (Protein Donor)	false
O3	CZ	ARG- 112	3.84	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 112	2.89	0	Ionic (Protein Cationic)	false
C11	CD1	LEU- 134	3.4	0	Hydrophobic	false
C10	CG2	THR- 168	3.57	0	Hydrophobic	false
C11	CB	ALA- 169	3.91	0	Hydrophobic	false
C8	CB	GLN- 172	4.22	0	Hydrophobic	false
C9	CG	GLN- 172	3.93	0	Hydrophobic	false
C10	CB	GLN- 172	3.85	0	Hydrophobic	false
O5	NZ	LYS- 212	2.59	174.96	H-Bond (Protein Donor)	false
O5	NZ	LYS- 212	2.59	0	Ionic (Protein Cationic)	false
O4	NZ	LYS- 212	3.89	0	Ionic (Protein Cationic)	false
C4	CD	LYS- 212	3.95	0	Hydrophobic	false
C5	CB	LYS- 212	4.22	0	Hydrophobic	false
O2	NZ	LYS- 269	3.25	149.24	H-Bond (Protein Donor)	false
O2	NZ	LYS- 269	3.25	0	Ionic (Protein Cationic)	false
O1	NZ	LYS- 269	3.1	0	Ionic (Protein Cationic)	false
O6	MG	MG- 4002	2.26	0	Metal Acceptor	false
O3	MG	MG- 4002	1.9	0	Metal Acceptor	false
O4	MG	MG- 4003	1.94	0	Metal Acceptor	false
O1	MG	MG- 4003	2.05	0	Metal Acceptor	false
O6	MG	MG- 4004	2.11	0	Metal Acceptor	false