scPDB - 2i76 entry

Protein Data Bank Entry:

PDB ID : 2i76

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2006-08-30

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:	Q9X250_THEMA
AC:	Q9X250
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	34.296
Number of residues:	35
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.671	901.125

% Hydrophobic	% Polar
39.70	60.30
According to VolSite

Ligand :

HET Code:	NDP
Formula:	C21H26N7O17P3
Molecular weight:	741.389 g/mol
DrugBank ID:	DB02338
Buried Surface Area:	52.15 %
Polar Surface area:	404.9 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	5
Rings:	5
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
2.26858	41.5921	1.67077

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
O3B	OG1	THR- 8	3.27	160.12	H-Bond (Protein Donor)	false
O2X	N	THR- 8	3.5	152.87	H-Bond (Protein Donor)	false
C5N	CD2	LEU- 11	4.12	0	Hydrophobic	false
O2X	OG	SER- 30	2.78	154.73	H-Bond (Protein Donor)	false
O3X	OG	SER- 30	3.08	132.91	H-Bond (Protein Donor)	false
O1X	N	ARG- 31	2.61	152.62	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 35	3.51	0	Ionic (Protein Cationic)	false
O3X	CZ	ARG- 35	2.96	0	Ionic (Protein Cationic)	false
C5D	CG2	ILE- 63	4.06	0	Hydrophobic	false
C4B	CG1	VAL- 64	4.42	0	Hydrophobic	false
C1B	CG1	VAL- 64	3.63	0	Hydrophobic	false
C3D	CD1	ILE- 69	4.46	0	Hydrophobic	false
C5N	CG	PRO- 105	3.74	0	Hydrophobic	false
O7N	N	PHE- 109	3.33	162.28	H-Bond (Protein Donor)	false