scPDB - 4zfn entry

Protein Data Bank Entry:

PDB ID : 4zfn

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2015-04-21

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Purine phosphoribosyltransferase (GpT-2)
ID:	Q97W22_SULSO
AC:	Q97W22
Organism:	Sulfolobus solfataricus
Reign:	Archaea
TaxID:	273057
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	100 %

Ligand binding site composition:

B-Factor:	38.241
Number of residues:	27
Including
Standard Amino Acids:	25
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.121	594.000

% Hydrophobic	% Polar
35.80	64.20
According to VolSite

Ligand :

HET Code:	5GP
Formula:	C10H12N5O8P
Molecular weight:	361.205 g/mol
DrugBank ID:	-
Buried Surface Area:	67.7 %
Polar Surface area:	217.22 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
23.6592	5.84621	33.6212

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
C5'	CD2	PHE- 63	4.29	0	Hydrophobic	false
C4'	CD	ARG- 65	4.4	0	Hydrophobic	false
C2'	CG1	VAL- 95	4.39	0	Hydrophobic	false
O1P	N	ASP- 97	3.23	128.69	H-Bond (Protein Donor)	false
C5'	CB	ASP- 97	3.3	0	Hydrophobic	false
O5'	OG1	THR- 98	3.1	164.42	H-Bond (Protein Donor)	false
C5'	CG2	THR- 98	4.19	0	Hydrophobic	false
O3P	N	THR- 101	2.87	146.8	H-Bond (Protein Donor)	false
O6	NZ	LYS- 125	2.93	143.17	H-Bond (Protein Donor)	false
O6	N	ILE- 143	3.15	159.62	H-Bond (Protein Donor)	false
N1	O	ILE- 143	2.74	157.37	H-Bond (Ligand Donor)	false
N2	O	ILE- 143	3.1	136.97	H-Bond (Ligand Donor)	false