scPDB - 1n4q entry

Protein Data Bank Entry:

PDB ID : 1n4q

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2002-11-01

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-1 subunit beta
ID:	PGTB1_RAT
AC:	P53610
Organism:	Rattus norvegicus
Reign:	Eukaryota
TaxID:	10116
EC Number:	2.5.1.59

Chains:

Chain Name:	Percentage of Residues within binding site
C	21 %
D	79 %

Ligand binding site composition:

B-Factor:	50.276
Number of residues:	34
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	ZN

Cavity properties

Ligandability	Volume (Å3)
0.979	1336.500

% Hydrophobic	% Polar
40.40	59.60
According to VolSite

Ligand :

HET Code:	LYS_CYS_VAL_ILE_LEU
Formula:	C26H51N6O6S
Molecular weight:	575.785 g/mol
DrugBank ID:	-
Buried Surface Area:	33.5 %
Polar Surface area:	250.6 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	7
Rings:	0
Aromatic rings:	0
Anionic atoms:	1
Cationic atoms:	2
Rule of Five Violation:	3
Rotatable Bonds:	19

Mass center Coordinates

X	Y	Z
-23.3209	29.3651	68.5619

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
CD1	CB	SER- 46	4.28	0	Hydrophobic	false
CD1	CG2	THR- 49	3.92	0	Hydrophobic	false
CD1	CZ	PHE- 53	4.34	0	Hydrophobic	false
CD1	CB	ALA- 123	4.02	0	Hydrophobic	false
CD2	CB	ALA- 123	3.89	0	Hydrophobic	false
CD1	CE	MET- 124	3.76	0	Hydrophobic	false
CG1	CD2	TYR- 166	4.42	0	Hydrophobic	false
O	NE2	GLN- 167	3.09	176.07	H-Bond (Protein Donor)	false
O	NH1	ARG- 173	2.74	148.21	H-Bond (Protein Donor)	false
CD2	CE2	PHE- 174	3.94	0	Hydrophobic	false
SG	SG	CYS- 271	4.05	0	Hydrophobic	false
O	NZ	LYS- 311	3.29	157.44	H-Bond (Protein Donor)	false
CB	CD2	LEU- 320	4.44	0	Hydrophobic	false
CG2	CD1	LEU- 320	4.1	0	Hydrophobic	false
CD1	CD1	LEU- 320	3.75	0	Hydrophobic	false
OXT	O	HOH- 1302	2.92	179.98	H-Bond (Protein Donor)	false