scPDB - 2e93 entry

Protein Data Bank Entry:

PDB ID : 2e93

Resolution :2.120 Å

Experimental Method : X-ray

Deposition Date : 2007-01-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	6.960	6.960	6.960	0.000	6.960	1

List of CHEMBLId :

CHEMBL411274

Binding Site :

Uniprot Annotation

Name:	Geranylgeranyl pyrophosphate synthase
ID:	GGPPS_YEAST
AC:	Q12051
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	37.020
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.050	1383.750

% Hydrophobic	% Polar
49.76	50.24
According to VolSite

Ligand :

HET Code:	B29
Formula:	C20H14O8P2
Molecular weight:	444.268 g/mol
DrugBank ID:	DB07410
Buried Surface Area:	62.53 %
Polar Surface area:	179.37 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	4
Aromatic rings:	4
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
35.8329	49.0996	8.1121

Binding mode :

What is Poseview ?

2D View
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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
CAS	CG	LYS- 41	3.75	0	Hydrophobic	false
OAG	N	LYS- 41	2.74	149.49	H-Bond (Protein Donor)	false
CAY	CG	ARG- 44	3.4	0	Hydrophobic	false
CAO	CB	ARG- 44	3.35	0	Hydrophobic	false
CAZ	CD	ARG- 44	3.22	0	Hydrophobic	false
DuAr	CZ	ARG- 44	3.57	161.4	Pi/Cation	false
CAQ	CD2	LEU- 47	4.29	0	Hydrophobic	false
CAP	CD1	ILE- 48	4.22	0	Hydrophobic	false
CAP	CG1	VAL- 69	3.29	0	Hydrophobic	false
CAY	CG1	VAL- 69	3.88	0	Hydrophobic	false
CAO	CG	GLU- 70	4.49	0	Hydrophobic	false
CAH	CB	GLU- 70	3.78	0	Hydrophobic	false
CAO	CB	HIS- 73	4.3	0	Hydrophobic	false
OAB	NE2	HIS- 73	2.69	157.23	H-Bond (Protein Donor)	false
OAD	NH1	ARG- 89	2.85	135.09	H-Bond (Protein Donor)	false
OAF	NE	ARG- 90	2.95	177.14	H-Bond (Protein Donor)	false
OAB	NH2	ARG- 90	2.96	150.91	H-Bond (Protein Donor)	false
OAF	CZ	ARG- 90	3.71	0	Ionic (Protein Cationic)	false
OAB	CZ	ARG- 90	3.87	0	Ionic (Protein Cationic)	false
CAN	CD2	LEU- 178	3.87	0	Hydrophobic	false
CAJ	CE2	TYR- 210	3.44	0	Hydrophobic	false
OAE	NZ	LYS- 228	2.96	144.1	H-Bond (Protein Donor)	false
OAE	NZ	LYS- 228	2.96	0	Ionic (Protein Cationic)	false