scPDB - 4r1f entry

Protein Data Bank Entry:

PDB ID : 4r1f

Resolution :2.510 Å

Experimental Method : X-ray

Deposition Date : 2014-08-05

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-alpha
ID:	TOP2A_HUMAN
AC:	P11388
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	5.99.1.3

Chains:

Chain Name:	Percentage of Residues within binding site
C	5 %
D	95 %

Ligand binding site composition:

B-Factor:	63.538
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.686	600.750

% Hydrophobic	% Polar
45.51	54.49
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	73.18 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
7.27556	52.4443	30.6093

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
O1A	ND2	ASN- 91	2.99	138.47	H-Bond (Protein Donor)	false
N6	OD1	ASN- 120	3.16	162.19	H-Bond (Ligand Donor)	false
C4'	CB	ILE- 141	4.16	0	Hydrophobic	false
C1'	CD1	ILE- 141	3.47	0	Hydrophobic	false
O2B	OG	SER- 148	2.59	163.11	H-Bond (Protein Donor)	false
C3'	CB	SER- 149	4.41	0	Hydrophobic	false
O3'	OG	SER- 149	2.9	148.1	H-Bond (Protein Donor)	false
O3'	N	SER- 149	2.78	128.61	H-Bond (Protein Donor)	false
O2'	OG	SER- 149	3.1	143.3	H-Bond (Protein Donor)	false
O2B	ND2	ASN- 150	2.92	140.53	H-Bond (Protein Donor)	false
O1B	N	ARG- 162	2.94	132.22	H-Bond (Protein Donor)	false
O1B	N	ASN- 163	3.33	120.59	H-Bond (Protein Donor)	false
O1B	N	GLY- 164	3.06	160.91	H-Bond (Protein Donor)	false
O2A	N	ALA- 167	2.73	155.84	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 168	3.01	166.38	H-Bond (Protein Donor)	false
O2A	NZ	LYS- 168	3.01	0	Ionic (Protein Cationic)	false
O3B	MG	MG- 501	2.14	0	Metal Acceptor	false
O1A	MG	MG- 501	2.15	0	Metal Acceptor	false