scPDB - 2z78 entry

Protein Data Bank Entry:

PDB ID : 2z78

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2007-08-16

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	98 %
B	2 %

Ligand binding site composition:

B-Factor:	25.189
Number of residues:	50
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.959	1292.625

% Hydrophobic	% Polar
38.64	61.36
According to VolSite

Ligand :

HET Code:	H86
Formula:	C23H30F2NO7P2
Molecular weight:	532.431 g/mol
DrugBank ID:	-
Buried Surface Area:	65.43 %
Polar Surface area:	159.1 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	0
Rings:	2
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	1
Rotatable Bonds:	15

Mass center Coordinates

X	Y	Z
30.5173	47.7174	9.86989

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
CAA	CB	ARG- 44	3.79	0	Hydrophobic	false
CAR	CG	ARG- 44	4.06	0	Hydrophobic	false
CAT	CD	ARG- 44	4.42	0	Hydrophobic	false
CAA	CD1	ILE- 48	3.43	0	Hydrophobic	false
CAP	CG1	ILE- 48	4.3	0	Hydrophobic	false
CAA	CG1	VAL- 69	3.25	0	Hydrophobic	false
CAK	CB	SER- 76	3.87	0	Hydrophobic	false
FAH	CB	ILE- 79	3.48	0	Hydrophobic	false
CAK	CB	ASP- 80	3.8	0	Hydrophobic	false
OAG	CZ	ARG- 89	3.92	0	Ionic (Protein Cationic)	false
OAC	CZ	ARG- 89	3.57	0	Ionic (Protein Cationic)	false
OAG	NH1	ARG- 89	3.02	169.55	H-Bond (Protein Donor)	false
OAC	NH2	ARG- 89	2.76	145.79	H-Bond (Protein Donor)	false
CAL	CD1	LEU- 143	4.3	0	Hydrophobic	false
FAI	CG	LEU- 143	3.31	0	Hydrophobic	false
CAJ	CG	GLN- 147	3.71	0	Hydrophobic	false
CBB	CB	GLN- 147	3.67	0	Hydrophobic	false
CAL	CG	LYS- 174	3.93	0	Hydrophobic	false
CAV	CG2	THR- 175	4.36	0	Hydrophobic	false
CAW	CB	THR- 175	4.31	0	Hydrophobic	false
CAX	CG2	THR- 175	3.77	0	Hydrophobic	false
CAS	CB	LEU- 178	4.19	0	Hydrophobic	false
CAV	CB	LEU- 178	4.29	0	Hydrophobic	false
CAQ	CD1	PHE- 179	4.49	0	Hydrophobic	false
CAS	CE2	PHE- 179	4.29	0	Hydrophobic	false
CAV	CE2	PHE- 179	3.55	0	Hydrophobic	false
CAP	CB	THR- 182	4.38	0	Hydrophobic	false
CAW	CE2	TYR- 210	3.47	0	Hydrophobic	false
OAB	NE2	GLN- 211	2.86	138.86	H-Bond (Protein Donor)	false
OAD	NZ	LYS- 238	3.37	125.51	H-Bond (Protein Donor)	false
OAD	NZ	LYS- 238	3.37	0	Ionic (Protein Cationic)	false
OAB	NZ	LYS- 238	2.64	0	Ionic (Protein Cationic)	false