scPDB - 2e8w entry

Protein Data Bank Entry:

PDB ID : 2e8w

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2007-01-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

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:	24.889
Number of residues:	29
Including
Standard Amino Acids:	24
Non Standard Amino Acids:	2
Water Molecules:	3
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.889	1147.500

% Hydrophobic	% Polar
39.41	60.59
According to VolSite

Ligand :

HET Code:	IPE
Formula:	C5H9O7P2
Molecular weight:	243.068 g/mol
DrugBank ID:	DB04714
Buried Surface Area:	58.91 %
Polar Surface area:	141.4 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	0
Rings:	0
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
28.5947	45.8126	7.41057

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
C4	CB	SER- 76	3.86	0	Hydrophobic	false
C2	CD2	LEU- 77	4.47	0	Hydrophobic	false
C2	CB	ASP- 80	4.3	0	Hydrophobic	false
O2B	NH1	ARG- 89	3.4	162.19	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 89	2.88	133.73	H-Bond (Protein Donor)	false
O3B	NH1	ARG- 89	3.33	122.89	H-Bond (Protein Donor)	false
O3B	CZ	ARG- 89	3.49	0	Ionic (Protein Cationic)	false
C4	CD1	LEU- 143	3.23	0	Hydrophobic	false
C1	CD	LYS- 174	4.28	0	Hydrophobic	false
O2A	NZ	LYS- 174	2.74	168.22	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 174	2.74	0	Ionic (Protein Cationic)	false
O3A	OD1	ASP- 214	3.29	133.44	H-Bond (Protein Donor)	false
O1B	OD1	ASP- 214	2.9	151.81	H-Bond (Protein Donor)	false
O1A	NZ	LYS- 238	3.64	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 238	2.66	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 238	2.66	156.69	H-Bond (Protein Donor)	false
O1A	MG	MG- 1201	2.03	0	Metal Acceptor	false
O1A	MG	MG- 1202	2.17	0	Metal Acceptor	false
O3B	MG	MG- 1202	2.21	0	Metal Acceptor	false