scPDB - 3pz3 entry

Protein Data Bank Entry:

PDB ID : 3pz3

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-12-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Geranylgeranyl transferase type-2 subunit beta
ID:	PGTB2_RAT
AC:	Q08603
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	2.5.1.60

Chains:

Chain Name:	Percentage of Residues within binding site
A	5 %
B	95 %

Ligand binding site composition:

B-Factor:	38.136
Number of residues:	42
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.914	567.000

% Hydrophobic	% Polar
48.81	51.19
According to VolSite

Ligand :

HET Code:	PZ3
Formula:	C41H39N5O7S
Molecular weight:	745.843 g/mol
DrugBank ID:	-
Buried Surface Area:	44.74 %
Polar Surface area:	144.58 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	1
Rings:	7
Aromatic rings:	6
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
4.24996	21.8034	25.667

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
NBG	ZN	ZN- 1	2.12	0	Metal Acceptor	false
DuAr	ZN	ZN- 1	3.17	106.49	Pi/Cation	false
CBA	CD2	LEU- 45	4.21	0	Hydrophobic	false
CAU	CD2	LEU- 45	3.7	0	Hydrophobic	false
CBE	CH2	TRP- 52	4	0	Hydrophobic	false
CAQ	CD2	LEU- 96	4.24	0	Hydrophobic	false
CAK	CD2	LEU- 99	3.66	0	Hydrophobic	false
CAQ	CD	ARG- 144	4.01	0	Hydrophobic	false
CBE	CE2	PHE- 289	3.49	0	Hydrophobic	false
CBA	CB	PHE- 289	3.93	0	Hydrophobic	false
CBF	CZ	PHE- 289	3.69	0	Hydrophobic	false
CAH	CB	CYS- 314	3.51	0	Hydrophobic	false