scPDB - 2z4z entry

Protein Data Bank Entry:

PDB ID : 2z4z

Resolution :2.090 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	94 %
B	6 %

Ligand binding site composition:

B-Factor:	33.863
Number of residues:	36
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.897	1218.375

% Hydrophobic	% Polar
41.55	58.45
According to VolSite

Ligand :

HET Code:	SC0
Formula:	C17H30O6P2
Molecular weight:	392.364 g/mol
DrugBank ID:	DB08529
Buried Surface Area:	64.82 %
Polar Surface area:	146 Å2

Number of
H-Bond Acceptors:	6
H-Bond Donors:	0
Rings:	0
Aromatic rings:	0
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	14

Mass center Coordinates

X	Y	Z
29.5243	46.8428	8.42136

Binding mode :

What is Poseview ?

2D View
3D View

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	CD	ARG- 44	3.69	0	Hydrophobic	false
CAN	CB	SER- 76	4.03	0	Hydrophobic	false
CAR	CD2	LEU- 77	4.13	0	Hydrophobic	false
OAF	OD2	ASP- 80	2.72	141.2	H-Bond (Protein Donor)	false
CAR	CB	ASP- 80	4.41	0	Hydrophobic	false
CAV	CB	ASP- 80	3.93	0	Hydrophobic	false
OAE	NH2	ARG- 89	2.7	150.1	H-Bond (Protein Donor)	false
OAE	NH1	ARG- 89	2.92	137.61	H-Bond (Protein Donor)	false
OAE	CZ	ARG- 89	3.23	0	Ionic (Protein Cationic)	false
CAT	CD1	LEU- 143	3.47	0	Hydrophobic	false
CAB	CG	LEU- 143	3.99	0	Hydrophobic	false
CAN	CG	GLN- 147	4.04	0	Hydrophobic	false
OAG	NZ	LYS- 174	2.93	165.25	H-Bond (Protein Donor)	false
OAG	NZ	LYS- 174	2.93	0	Ionic (Protein Cationic)	false
OAH	NZ	LYS- 174	3.14	0	Ionic (Protein Cationic)	false
CAP	CG	LYS- 174	4.33	0	Hydrophobic	false
CAU	CG2	THR- 175	3.62	0	Hydrophobic	false
CAO	CD1	LEU- 178	4.07	0	Hydrophobic	false
CAP	CD1	LEU- 178	4.38	0	Hydrophobic	false
CAM	CE2	PHE- 179	3.83	0	Hydrophobic	false
CAU	CE2	PHE- 179	3.92	0	Hydrophobic	false
CAM	CZ	TYR- 210	4.31	0	Hydrophobic	false
CAQ	CE2	TYR- 210	4.42	0	Hydrophobic	false
CAU	CE2	TYR- 210	3.85	0	Hydrophobic	false
OAD	NE2	GLN- 211	3.29	141.23	H-Bond (Protein Donor)	false
OAG	NZ	LYS- 238	3.96	0	Ionic (Protein Cationic)	false
OAD	NZ	LYS- 238	2.6	0	Ionic (Protein Cationic)	false
OAD	NZ	LYS- 238	2.6	145.25	H-Bond (Protein Donor)	false
CAA	CB	LEU- 340	3.72	0	Hydrophobic	false
OAC	MG	MG- 1301	2	0	Metal Acceptor	false
OAD	MG	MG- 1301	2.03	0	Metal Acceptor	false