scPDB - 1pvg entry

Protein Data Bank Entry:

PDB ID : 1pvg

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 2003-06-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA topoisomerase 2
ID:	TOP2_YEAST
AC:	P06786
Organism:	Saccharomyces cerevisiae
Reign:	Eukaryota
TaxID:	559292
EC Number:	5.99.1.3

Chains:

Chain Name:	Percentage of Residues within binding site
A	97 %
B	3 %

Ligand binding site composition:

B-Factor:	15.518
Number of residues:	40
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.718	570.375

% Hydrophobic	% Polar
40.24	59.76
According to VolSite

Ligand :

HET Code:	ANP
Formula:	C10H13N6O12P3
Molecular weight:	502.164 g/mol
DrugBank ID:	-
Buried Surface Area:	77.78 %
Polar Surface area:	322.68 Å2

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

Mass center Coordinates

X	Y	Z
23.4227	46.4505	41.6541

Binding mode :

What is Poseview ?

2D View
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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
O1A	ND2	ASN- 70	2.87	146.97	H-Bond (Protein Donor)	false
N6	OD1	ASN- 99	2.9	163.4	H-Bond (Ligand Donor)	false
C5'	CB	ILE- 120	4.35	0	Hydrophobic	false
C4'	CD1	ILE- 120	4.1	0	Hydrophobic	false
C1'	CD1	ILE- 120	3.7	0	Hydrophobic	false
O2B	OG	SER- 127	2.71	151.83	H-Bond (Protein Donor)	false
O3'	OG	SER- 127	3.42	129.29	H-Bond (Ligand Donor)	false
O3'	N	SER- 128	3	173.07	H-Bond (Protein Donor)	false
O2'	OG	SER- 128	2.68	156.34	H-Bond (Protein Donor)	false
O2B	ND2	ASN- 129	2.98	156.44	H-Bond (Protein Donor)	false
O3G	N	ARG- 141	2.91	159.2	H-Bond (Protein Donor)	false
O3G	N	ASN- 142	3.19	171.14	H-Bond (Protein Donor)	false
O1G	N	TYR- 144	2.81	159.34	H-Bond (Protein Donor)	false
O1G	N	GLY- 145	2.86	156.51	H-Bond (Protein Donor)	false
O1A	N	ALA- 146	3.06	134.01	H-Bond (Protein Donor)	false
O2A	N	ALA- 146	2.89	155.57	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 147	2.7	154.08	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 147	2.7	0	Ionic (Protein Cationic)	false
O1G	NE2	GLN- 365	3.05	149.45	H-Bond (Protein Donor)	false
O2G	NZ	LYS- 367	3.66	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 367	2.62	0	Ionic (Protein Cationic)	false
O3G	NZ	LYS- 367	2.62	154.37	H-Bond (Protein Donor)	false
O2G	MG	MG- 903	1.98	0	Metal Acceptor	false
O1B	MG	MG- 903	2.11	0	Metal Acceptor	false
O1A	MG	MG- 903	2.15	0	Metal Acceptor	false