scPDB - 3g6x entry

Protein Data Bank Entry:

PDB ID : 3g6x

Resolution :2.080 Å

Experimental Method : X-ray

Deposition Date : 2009-02-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA polymerase iota
ID:	POLI_HUMAN
AC:	Q9UNA4
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	2.7.7.7

Chains:

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

Ligand binding site composition:

B-Factor:	22.566
Number of residues:	25
Including
Standard Amino Acids:	22
Non Standard Amino Acids:	2
Water Molecules:	1
Cofactors:
Metals:	MG MG

Cavity properties

Ligandability	Volume (Å3)
0.343	621.000

% Hydrophobic	% Polar
37.50	62.50
According to VolSite

Ligand :

HET Code:	DGT
Formula:	C10H12N5O13P3
Molecular weight:	503.149 g/mol
DrugBank ID:	DB02181
Buried Surface Area:	52.78 %
Polar Surface area:	315.33 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	3
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
1.61165	23.329	17.7056

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
O3G	N	CYS- 37	2.83	176.9	H-Bond (Protein Donor)	false
O1B	N	PHE- 38	3.36	125.91	H-Bond (Protein Donor)	false
O2B	N	PHE- 38	3.03	167.09	H-Bond (Protein Donor)	false
C5'	CB	PHE- 38	4.28	0	Hydrophobic	false
C4'	CE1	TYR- 39	4.05	0	Hydrophobic	false
C3'	CD1	TYR- 39	4.28	0	Hydrophobic	false
C2'	CE2	TYR- 39	3.95	0	Hydrophobic	false
C1'	CZ	TYR- 39	3.75	0	Hydrophobic	false
O3'	N	TYR- 39	3.08	164.54	H-Bond (Protein Donor)	false
N2	OE1	GLN- 59	2.86	139.15	H-Bond (Ligand Donor)	false
O1B	OG1	THR- 65	2.67	174.72	H-Bond (Protein Donor)	false
C3'	CB	THR- 65	4.26	0	Hydrophobic	false
O3G	OH	TYR- 68	2.59	148.55	H-Bond (Protein Donor)	false
O2G	NH1	ARG- 71	3.02	169.16	H-Bond (Protein Donor)	false
O3B	NH2	ARG- 71	2.9	164.22	H-Bond (Protein Donor)	false
O2G	CZ	ARG- 71	3.75	0	Ionic (Protein Cationic)	false
O3G	CZ	ARG- 71	3.94	0	Ionic (Protein Cationic)	false
O2G	NZ	LYS- 77	2.63	171.76	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 77	2.63	0	Ionic (Protein Cationic)	false
C5'	CB	ASP- 126	4.34	0	Hydrophobic	false
O2G	NZ	LYS- 214	2.81	169.92	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 214	2.81	0	Ionic (Protein Cationic)	false
O1G	MG	MG- 871	2.45	0	Metal Acceptor	false
O2B	MG	MG- 871	2.38	0	Metal Acceptor	false
O1A	MG	MG- 871	2.06	0	Metal Acceptor	false