scPDB - 2z7h entry

Protein Data Bank Entry:

PDB ID : 2z7h

Resolution :2.080 Å

Experimental Method : X-ray

Deposition Date : 2007-08-23

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:	38.336
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
1.074	715.500

% Hydrophobic	% Polar
52.36	47.64
According to VolSite

Ligand :

HET Code:	GG3
Formula:	C14H22NO7P2
Molecular weight:	378.274 g/mol
DrugBank ID:	-
Buried Surface Area:	56.99 %
Polar Surface area:	170.67 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	2
Rings:	1
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
31.0672	47.9023	7.40792

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
C31	CD	ARG- 44	3.39	0	Hydrophobic	false
C30	CG	ARG- 44	3.78	0	Hydrophobic	false
C29	CD	ARG- 44	4.37	0	Hydrophobic	false
C7	CD2	LEU- 77	4.45	0	Hydrophobic	false
C22	CD2	LEU- 77	4.04	0	Hydrophobic	false
O16	NH2	ARG- 89	3.2	138	H-Bond (Protein Donor)	false
O15	NH2	ARG- 89	3.39	130.63	H-Bond (Protein Donor)	false
O15	NH1	ARG- 89	2.8	160.33	H-Bond (Protein Donor)	false
O15	CZ	ARG- 89	3.53	0	Ionic (Protein Cationic)	false
O12	NZ	LYS- 174	2.58	160.49	H-Bond (Protein Donor)	false
O12	NZ	LYS- 174	2.58	0	Ionic (Protein Cationic)	false
C33	CD1	LEU- 178	4.17	0	Hydrophobic	false
C27	CE2	PHE- 179	4.39	0	Hydrophobic	false
C22	CE2	TYR- 210	4.26	0	Hydrophobic	false
C26	CZ	TYR- 210	4.15	0	Hydrophobic	false
C27	CE2	TYR- 210	3.72	0	Hydrophobic	false
O17	OD1	ASP- 214	2.79	175.15	H-Bond (Protein Donor)	false
O10	NZ	LYS- 238	2.64	148.85	H-Bond (Protein Donor)	false
O12	NZ	LYS- 238	3.39	140.87	H-Bond (Protein Donor)	false
O10	NZ	LYS- 238	2.64	0	Ionic (Protein Cationic)	false
O12	NZ	LYS- 238	3.39	0	Ionic (Protein Cationic)	false
O16	MG	MG- 1301	1.97	0	Metal Acceptor	false
O11	MG	MG- 1301	2.35	0	Metal Acceptor	false