scPDB - 2zev entry

Protein Data Bank Entry:

PDB ID : 2zev

Resolution :2.230 Å

Experimental Method : X-ray

Deposition Date : 2007-12-17

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:	42.440
Number of residues:	38
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
1.053	580.500

% Hydrophobic	% Polar
61.63	38.37
According to VolSite

Ligand :

HET Code:	B71
Formula:	C17H28NO7P2
Molecular weight:	420.354 g/mol
DrugBank ID:	-
Buried Surface Area:	61.21 %
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:	14

Mass center Coordinates

X	Y	Z
30.9664	48.2998	8.53081

Binding mode :

What is Poseview ?

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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
CAM	CG	ARG- 44	3.99	0	Hydrophobic	false
CAA	CD2	LEU- 47	3.73	0	Hydrophobic	false
CAA	CG1	ILE- 48	4.02	0	Hydrophobic	false
CAM	CG1	VAL- 69	3.56	0	Hydrophobic	false
OAF	NH2	ARG- 89	2.85	136.01	H-Bond (Protein Donor)	false
OAC	NH2	ARG- 89	3.43	127.39	H-Bond (Protein Donor)	false
OAC	NH1	ARG- 89	2.65	169	H-Bond (Protein Donor)	false
OAF	CZ	ARG- 89	3.69	0	Ionic (Protein Cationic)	false
OAC	CZ	ARG- 89	3.49	0	Ionic (Protein Cationic)	false
CAI	CD1	LEU- 143	3.6	0	Hydrophobic	false
OAB	NZ	LYS- 174	3.06	159.91	H-Bond (Protein Donor)	false
OAB	NZ	LYS- 174	3.06	0	Ionic (Protein Cationic)	false
CAH	CG	LYS- 174	3.57	0	Hydrophobic	false
CAT	CG2	THR- 175	3.6	0	Hydrophobic	false
CAL	CD1	PHE- 179	4.25	0	Hydrophobic	false
CAQ	CZ	PHE- 179	3.27	0	Hydrophobic	false
CAR	CE2	PHE- 179	3.99	0	Hydrophobic	false
CAA	CG2	THR- 182	3.44	0	Hydrophobic	false
CAL	CB	THR- 182	4.13	0	Hydrophobic	false
CAQ	CZ	TYR- 210	3.92	0	Hydrophobic	false
CAR	CE2	TYR- 210	3.34	0	Hydrophobic	false
OAD	NE2	GLN- 211	3.43	142.85	H-Bond (Protein Donor)	false
OAG	OD1	ASP- 214	2.82	156.67	H-Bond (Protein Donor)	false
OAD	OD1	ASP- 214	3.03	129.07	H-Bond (Protein Donor)	false
OAG	NZ	LYS- 238	3.92	0	Ionic (Protein Cationic)	false
OAE	NZ	LYS- 238	3.35	0	Ionic (Protein Cationic)	false
OAE	NZ	LYS- 238	3.35	127.34	H-Bond (Protein Donor)	false
OAE	MG	MG- 1301	2.23	0	Metal Acceptor	false
OAF	MG	MG- 1302	2.15	0	Metal Acceptor	false
OAE	MG	MG- 1302	2.14	0	Metal Acceptor	false