scPDB - 2xjc entry

Protein Data Bank Entry:

PDB ID : 2xjc

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2010-07-03

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Cytosolic purine 5'-nucleotidase
ID:	5NTC_HUMAN
AC:	P49902
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.1.3.5

Chains:

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

Ligand binding site composition:

B-Factor:	23.740
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)
0.230	607.500

% Hydrophobic	% Polar
41.11	58.89
According to VolSite

Ligand :

HET Code:	5GP
Formula:	C10H12N5O8P
Molecular weight:	361.205 g/mol
DrugBank ID:	-
Buried Surface Area:	61.58 %
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
2.76021	15.1573	41.6228

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
O2P	ND2	ASN- 52	3.31	133.24	H-Bond (Protein Donor)	false
O3P	ND2	ASN- 52	2.55	146.46	H-Bond (Protein Donor)	false
O1P	N	MET- 53	3.27	135.2	H-Bond (Protein Donor)	false
O1P	N	ASP- 54	2.93	174.24	H-Bond (Protein Donor)	false
C5'	CB	ASP- 54	3.44	0	Hydrophobic	false
C5'	CE2	PHE- 157	4.24	0	Hydrophobic	false
C2'	CZ	PHE- 157	4.1	0	Hydrophobic	false
O6	NH2	ARG- 202	2.94	155.83	H-Bond (Protein Donor)	false
N1	OD1	ASP- 206	2.67	167.37	H-Bond (Ligand Donor)	false
N2	OD1	ASP- 206	3.49	125.53	H-Bond (Ligand Donor)	false
O3'	NZ	LYS- 215	3.43	134.55	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 215	2.76	142.17	H-Bond (Protein Donor)	false
O1P	OG1	THR- 249	2.65	154.91	H-Bond (Protein Donor)	false
O3P	N	ASN- 250	2.85	163.97	H-Bond (Protein Donor)	false
O5'	N	ASN- 250	3.48	132.78	H-Bond (Protein Donor)	false
C4'	CB	ASN- 250	4.14	0	Hydrophobic	false
C3'	CB	SER- 251	3.75	0	Hydrophobic	false
O3P	NZ	LYS- 292	2.76	158.82	H-Bond (Protein Donor)	false
O3P	NZ	LYS- 292	2.76	0	Ionic (Protein Cationic)	false
O2P	MG	MG- 1499	1.92	0	Metal Acceptor	false
O6	O	HOH- 2368	2.97	130.7	H-Bond (Protein Donor)	false