scPDB - 3q23 entry

Protein Data Bank Entry:

PDB ID : 3q23

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2010-12-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Virion DNA-directed RNA polymerase
ID:	RPOLV_BPN4
AC:	Q859P9
Organism:	Enterobacteria phage N4
Reign:	Viruses
TaxID:	10752
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.468
Number of residues:	30
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	3
Water Molecules:	1
Cofactors:
Metals:	MN MN

Cavity properties

Ligandability	Volume (Å3)
0.001	668.250

% Hydrophobic	% Polar
38.89	61.11
According to VolSite

Ligand :

HET Code:	G2P
Formula:	C11H14N5O13P3
Molecular weight:	517.176 g/mol
DrugBank ID:	DB03532
Buried Surface Area:	50.64 %
Polar Surface area:	326.33 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
12.1725	-80.6617	229.319

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
O4'	NH2	ARG- 424	3.27	144.91	H-Bond (Protein Donor)	false
O3G	N	THR- 562	2.8	171.32	H-Bond (Protein Donor)	false
O1B	N	ASN- 563	3.06	173.24	H-Bond (Protein Donor)	false
C5'	CB	ASN- 563	4.34	0	Hydrophobic	false
O3'	N	GLY- 564	2.76	157.09	H-Bond (Protein Donor)	false
O2B	OH	TYR- 612	2.63	162.54	H-Bond (Protein Donor)	false
O2G	NH2	ARG- 666	3.02	158.05	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 666	3.93	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 670	3.92	0	Ionic (Protein Cationic)	false
O6	ND2	ASN- 671	3.16	148.59	H-Bond (Protein Donor)	false
C2'	CG2	THR- 674	3.88	0	Hydrophobic	false
C2'	CE1	TYR- 678	4.13	0	Hydrophobic	false
O2'	OH	TYR- 678	2.82	175.23	H-Bond (Protein Donor)	false
C5'	CB	ASP- 951	4.01	0	Hydrophobic	false
O2A	MN	MN- 1107	2.33	0	Metal Acceptor	false
O1G	MN	MN- 1109	2.23	0	Metal Acceptor	false
O1B	MN	MN- 1109	2.13	0	Metal Acceptor	false
O2A	MN	MN- 1109	2.29	0	Metal Acceptor	false
O2'	O	HOH- 1128	2.69	152.06	H-Bond (Ligand Donor)	false