scPDB - 5da9 entry

Protein Data Bank Entry:

PDB ID : 5da9

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2015-08-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein
ID:	G0SHW7_CHATD
AC:	G0SHW7
Organism:	Chaetomium thermophilum
Reign:	Eukaryota
TaxID:	759272
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	30 %
B	70 %

Ligand binding site composition:

B-Factor:	87.315
Number of residues:	46
Including
Standard Amino Acids:	45
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.774	661.500

% Hydrophobic	% Polar
42.35	57.65
According to VolSite

Ligand :

HET Code:	AGS
Formula:	C10H14N5O12P3S
Molecular weight:	521.231 g/mol
DrugBank ID:	DB02930
Buried Surface Area:	76.52 %
Polar Surface area:	329.24 Å2

Number of
H-Bond Acceptors:	17
H-Bond Donors:	5
Rings:	3
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-40.4511	-15.5265	-39.0425

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
N7	NH1	ARG- 13	3.24	172.37	H-Bond (Protein Donor)	false
C4'	CB	SER- 14	4.41	0	Hydrophobic	false
C1'	CB	SER- 14	3.85	0	Hydrophobic	false
O2G	ND2	ASN- 36	2.99	133.02	H-Bond (Protein Donor)	false
O3B	N	GLY- 37	2.79	155.92	H-Bond (Protein Donor)	false
O3'	O	GLY- 37	3.33	173.53	H-Bond (Ligand Donor)	false
O2B	N	GLY- 39	3.26	158.2	H-Bond (Protein Donor)	false
O3A	N	GLY- 39	3.18	127.7	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 40	3.35	0	Ionic (Protein Cationic)	false
O2B	N	LYS- 40	2.89	149.48	H-Bond (Protein Donor)	false
O1B	N	THR- 41	3.27	155.62	H-Bond (Protein Donor)	false
O2A	OG1	THR- 42	2.71	168.89	H-Bond (Protein Donor)	false
O2A	N	THR- 42	2.75	142.43	H-Bond (Protein Donor)	false
N6	O	ILE- 66	2.81	123.25	H-Bond (Ligand Donor)	false
N1	N	ASP- 68	3.33	135.09	H-Bond (Protein Donor)	false
O3B	OG	SER- 1208	2.77	164.24	H-Bond (Protein Donor)	false
C5'	CB	SER- 1208	4.19	0	Hydrophobic	false
C3'	CB	SER- 1208	4.25	0	Hydrophobic	false
O2G	N	GLY- 1210	2.8	155	H-Bond (Protein Donor)	false
O3'	NE2	GLN- 1211	2.7	135.71	H-Bond (Protein Donor)	false
O3G	MG	MG- 1401	1.99	0	Metal Acceptor	false
O1B	MG	MG- 1401	2.42	0	Metal Acceptor	false