scPDB - 2z4y entry

Protein Data Bank Entry:

PDB ID : 2z4y

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2007-06-26

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	93 %
B	7 %

Ligand binding site composition:

B-Factor:	28.301
Number of residues:	32
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.038	685.125

% Hydrophobic	% Polar
53.69	46.31
According to VolSite

Ligand :

HET Code:	252
Formula:	C9H18O7P2
Molecular weight:	300.183 g/mol
DrugBank ID:	DB06931
Buried Surface Area:	61.14 %
Polar Surface area:	166.23 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	1
Rings:	0
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	9

Mass center Coordinates

X	Y	Z
27.6018	46.0276	8.00967

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
CAI	CB	SER- 76	4.45	0	Hydrophobic	false
CAK	CB	SER- 76	4.01	0	Hydrophobic	false
CAM	CD2	LEU- 77	4.3	0	Hydrophobic	false
CAO	CD2	LEU- 77	4.15	0	Hydrophobic	false
CAK	CB	ASP- 80	4.07	0	Hydrophobic	false
CAM	CB	ASP- 80	4.05	0	Hydrophobic	false
OAE	NH2	ARG- 89	2.97	136.09	H-Bond (Protein Donor)	false
OAE	NH1	ARG- 89	2.66	153.41	H-Bond (Protein Donor)	false
OAE	CZ	ARG- 89	3.24	0	Ionic (Protein Cationic)	false
CAA	CG	LEU- 143	3.72	0	Hydrophobic	false
CAI	CD2	LEU- 143	4.19	0	Hydrophobic	false
CAJ	CG	LEU- 143	3.83	0	Hydrophobic	false
CAA	CB	GLN- 147	4	0	Hydrophobic	false
CAJ	CG	GLN- 147	3.99	0	Hydrophobic	false
CAL	CG	LYS- 174	4.47	0	Hydrophobic	false
OAG	NZ	LYS- 174	3.09	149.67	H-Bond (Protein Donor)	false
OAG	NZ	LYS- 174	3.09	0	Ionic (Protein Cationic)	false
OAC	NZ	LYS- 174	3.97	0	Ionic (Protein Cationic)	false
OAH	NE2	GLN- 211	2.71	169.06	H-Bond (Protein Donor)	false
OAG	NZ	LYS- 238	3.95	0	Ionic (Protein Cationic)	false
OAH	NZ	LYS- 238	2.67	0	Ionic (Protein Cationic)	false
OAC	NZ	LYS- 238	2.91	0	Ionic (Protein Cationic)	false
OAB	O	HOH- 1395	2.96	143.87	H-Bond (Protein Donor)	false