scPDB - 2z4w entry

Protein Data Bank Entry:

PDB ID : 2z4w

Resolution :2.450 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	97 %
B	3 %

Ligand binding site composition:

B-Factor:	36.956
Number of residues:	40
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.729	718.875

% Hydrophobic	% Polar
54.46	45.54
According to VolSite

Ligand :

HET Code:	749
Formula:	C21H34O6P2
Molecular weight:	444.439 g/mol
DrugBank ID:	-
Buried Surface Area:	65.96 %
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:	12

Mass center Coordinates

X	Y	Z
29.9453	46.9397	8.52921

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
CAC	CG	ARG- 44	3.79	0	Hydrophobic	false
CAA	CB	SER- 76	4.27	0	Hydrophobic	false
CAE	CB	SER- 76	4.27	0	Hydrophobic	false
CAQ	CB	SER- 76	4	0	Hydrophobic	false
CAE	CD2	LEU- 77	4.01	0	Hydrophobic	false
CAA	CG2	ILE- 79	4.04	0	Hydrophobic	false
CAQ	CB	ASP- 80	4.24	0	Hydrophobic	false
CAS	CB	ASP- 80	4.28	0	Hydrophobic	false
OAH	CZ	ARG- 89	3.63	0	Ionic (Protein Cationic)	false
OAK	CZ	ARG- 89	4	0	Ionic (Protein Cationic)	false
OAH	NH1	ARG- 89	2.76	174.64	H-Bond (Protein Donor)	false
OAK	NH2	ARG- 89	3.28	146.33	H-Bond (Protein Donor)	false
CAB	CG	LEU- 143	3.55	0	Hydrophobic	false
CAU	CD1	LEU- 143	4.23	0	Hydrophobic	false
CAA	CG	GLN- 147	4.38	0	Hydrophobic	false
CAB	CB	GLN- 147	3.61	0	Hydrophobic	false
OAI	NZ	LYS- 174	3.3	158.98	H-Bond (Protein Donor)	false
OAI	NZ	LYS- 174	3.3	0	Ionic (Protein Cationic)	false
CAU	CG	LYS- 174	3.86	0	Hydrophobic	false
CAF	CG2	THR- 175	4.21	0	Hydrophobic	false
CAD	CB	LEU- 178	4.06	0	Hydrophobic	false
CAD	CE2	PHE- 179	3.68	0	Hydrophobic	false
CAV	CE2	TYR- 210	3.81	0	Hydrophobic	false
OAJ	OD1	ASP- 214	3.3	127.9	H-Bond (Protein Donor)	false
OAL	OD1	ASP- 214	2.9	152.05	H-Bond (Protein Donor)	false
OAG	NZ	LYS- 238	3.84	0	Ionic (Protein Cationic)	false
OAI	NZ	LYS- 238	3.12	0	Ionic (Protein Cationic)	false
OAI	NZ	LYS- 238	3.12	120.99	H-Bond (Protein Donor)	false
OAG	MG	MG- 1301	2.28	0	Metal Acceptor	false
OAG	MG	MG- 1302	2.04	0	Metal Acceptor	false
OAK	MG	MG- 1302	2.08	0	Metal Acceptor	false