scPDB - 2z52 entry

Protein Data Bank Entry:

PDB ID : 2z52

Resolution :2.130 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	9 %
B	91 %

Ligand binding site composition:

B-Factor:	22.631
Number of residues:	38
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	3
Water Molecules:	3
Cofactors:
Metals:	MG MG MG

Cavity properties

Ligandability	Volume (Å3)
0.660	820.125

% Hydrophobic	% Polar
51.85	48.15
According to VolSite

Ligand :

HET Code:	H23
Formula:	C12H24O7P2
Molecular weight:	342.262 g/mol
DrugBank ID:	DB07873
Buried Surface Area:	63.48 %
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:	12

Mass center Coordinates

X	Y	Z
25.3798	28.5462	28.777

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
CAA	CD2	LEU- 72	4.19	0	Hydrophobic	false
CAN	CB	SER- 76	3.94	0	Hydrophobic	false
CAI	CB	SER- 76	3.6	0	Hydrophobic	false
CAK	CB	SER- 76	3.41	0	Hydrophobic	false
CAR	CD2	LEU- 77	4.37	0	Hydrophobic	false
CAP	CB	ASP- 80	3.91	0	Hydrophobic	false
CAR	CB	ASP- 80	4.31	0	Hydrophobic	false
OAE	NH2	ARG- 89	3.37	148.02	H-Bond (Protein Donor)	false
OAB	NH1	ARG- 89	2.87	159.25	H-Bond (Protein Donor)	false
OAB	NH2	ARG- 89	3.24	137.47	H-Bond (Protein Donor)	false
OAB	CZ	ARG- 89	3.49	0	Ionic (Protein Cationic)	false
CAA	CE2	TYR- 112	4.1	0	Hydrophobic	false
CAI	CZ	TYR- 112	3.48	0	Hydrophobic	false
CAA	CD1	LEU- 140	3.49	0	Hydrophobic	false
CAA	CD1	LEU- 143	3.53	0	Hydrophobic	false
CAL	CB	LEU- 143	4.2	0	Hydrophobic	false
CAM	CB	GLN- 147	3.83	0	Hydrophobic	false
CAO	CG	LYS- 174	4.13	0	Hydrophobic	false
OAC	NZ	LYS- 174	2.87	162.21	H-Bond (Protein Donor)	false
OAC	NZ	LYS- 174	2.87	0	Ionic (Protein Cationic)	false
OAG	NZ	LYS- 238	2.83	162.75	H-Bond (Protein Donor)	false
OAG	NZ	LYS- 238	2.83	0	Ionic (Protein Cationic)	false
OAC	NZ	LYS- 238	3.65	0	Ionic (Protein Cationic)	false
OAE	MG	MG- 1304	1.95	0	Metal Acceptor	false
OAH	MG	MG- 1304	1.98	0	Metal Acceptor	false
OAH	MG	MG- 1305	2.07	0	Metal Acceptor	false
OAF	MG	MG- 1306	2.03	0	Metal Acceptor	false
OAG	MG	MG- 1306	2.1	0	Metal Acceptor	false
OAC	O	HOH- 1562	2.74	178.32	H-Bond (Protein Donor)	false