scPDB - 1cy1 entry

Protein Data Bank Entry:

PDB ID : 1cy1

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 1999-08-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	DNA topoisomerase 1
ID:	TOP1_ECOLI
AC:	P06612
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	30.179
Number of residues:	27
Including
Standard Amino Acids:	27
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.434	1059.750

% Hydrophobic	% Polar
35.03	64.97
According to VolSite

Ligand :

HET Code:	TMP
Formula:	C10H13N2O8P
Molecular weight:	320.193 g/mol
DrugBank ID:	-
Buried Surface Area:	56.95 %
Polar Surface area:	161.1 Å2

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

Mass center Coordinates

X	Y	Z
40.4475	19.8642	41.5093

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
C5M	CB	ASP- 113	3.52	0	Hydrophobic	false
O2P	NH2	ARG- 114	3.12	170.12	H-Bond (Protein Donor)	false
C1'	CD	ARG- 114	4.07	0	Hydrophobic	false
C5M	CB	ARG- 114	3.96	0	Hydrophobic	false
C5'	CG	ARG- 114	3.43	0	Hydrophobic	false
O3P	CZ	ARG- 161	3.91	0	Ionic (Protein Cationic)	false
O3P	NE	ARG- 161	2.81	144.98	H-Bond (Protein Donor)	false
O5'	NH2	ARG- 161	3.13	138.52	H-Bond (Protein Donor)	false
O5'	NE	ARG- 161	3.28	135.58	H-Bond (Protein Donor)	false
C2'	CG	ARG- 493	4.29	0	Hydrophobic	false
C5M	CB	SER- 495	3.69	0	Hydrophobic	false