scPDB - 4col entry

Protein Data Bank Entry:

PDB ID : 4col

Resolution :1.960 Å

Experimental Method : X-ray

Deposition Date : 2014-01-29

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:	Q9WYL6_THEMA
AC:	Q9WYL6
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	53 %
B	47 %

Ligand binding site composition:

B-Factor:	39.885
Number of residues:	31
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.193	550.125

% Hydrophobic	% Polar
38.65	61.35
According to VolSite

Ligand :

HET Code:	DTP
Formula:	C10H12N5O12P3
Molecular weight:	487.150 g/mol
DrugBank ID:	DB03222
Buried Surface Area:	72.36 %
Polar Surface area:	299.64 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	2
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-15.0618	14.3793	36.0175

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
C4'	CB	SER- 146	4.38	0	Hydrophobic	false
C1'	CB	SER- 146	3.87	0	Hydrophobic	false
N3	OG	SER- 146	2.52	144.02	H-Bond (Protein Donor)	false
O3'	N	GLU- 147	2.8	161.56	H-Bond (Protein Donor)	false
C4'	CB	GLU- 147	4.17	0	Hydrophobic	false
O1B	NZ	LYS- 150	2.85	146.62	H-Bond (Protein Donor)	false
O1A	N	LYS- 150	2.76	163.5	H-Bond (Protein Donor)	false
O1B	NZ	LYS- 150	2.85	0	Ionic (Protein Cationic)	false
O1G	NE2	HIS- 151	2.77	166.94	H-Bond (Protein Donor)	false
O1A	OG1	THR- 154	2.66	162.33	H-Bond (Protein Donor)	false
C5'	CG2	THR- 154	4.41	0	Hydrophobic	false
O4'	NE2	HIS- 158	2.87	148.27	H-Bond (Protein Donor)	false
O1G	NE1	TRP- 203	3.49	146.34	H-Bond (Protein Donor)	false
O2G	NE1	TRP- 203	3.25	152.01	H-Bond (Protein Donor)	false
O2A	NE2	GLN- 207	2.89	144.68	H-Bond (Protein Donor)	false
O2B	NE2	GLN- 210	2.93	141.01	H-Bond (Protein Donor)	false
C2'	CG	GLN- 210	4.26	0	Hydrophobic	false
C1'	CD2	TYR- 214	3.73	0	Hydrophobic	false
C2'	CE2	TYR- 214	3.58	0	Hydrophobic	false
N6	OG	SER- 215	3.05	138.77	H-Bond (Ligand Donor)	false
O2G	MG	MG- 701	2.06	0	Metal Acceptor	false
O2B	MG	MG- 701	2.09	0	Metal Acceptor	false
O2A	MG	MG- 701	2.02	0	Metal Acceptor	false