scPDB - 2np6 entry

Protein Data Bank Entry:

PDB ID : 2np6

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2006-10-26

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Modification methylase TaqI
ID:	MTTA_THEAQ
AC:	P14385
Organism:	Thermus aquaticus
Reign:	Bacteria
TaxID:	271
EC Number:	2.1.1.72

Chains:

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

Ligand binding site composition:

B-Factor:	7.598
Number of residues:	29
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.693	459.000

% Hydrophobic	% Polar
55.88	44.12
According to VolSite

Ligand :

HET Code:	NEA
Formula:	C12H19N6O3S
Molecular weight:	327.383 g/mol
DrugBank ID:	-
Buried Surface Area:	57.16 %
Polar Surface area:	172.25 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	4
Rings:	3
Aromatic rings:	2
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	5

Mass center Coordinates

X	Y	Z
47.0259	-29.3841	16.2015

Binding mode :

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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
CG	CB	VAL- 21	4.07	0	Hydrophobic	false
SD	CB	ALA- 47	4.04	0	Hydrophobic	false
C4'	CB	ALA- 47	4.19	0	Hydrophobic	false
C1'	CB	ALA- 47	3.95	0	Hydrophobic	false
O3'	OE2	GLU- 71	3.46	122.82	H-Bond (Ligand Donor)	false
O3'	OE1	GLU- 71	3.05	154.72	H-Bond (Ligand Donor)	false
O2'	OE2	GLU- 71	2.69	152.53	H-Bond (Ligand Donor)	false
N3	N	ILE- 72	3.41	132.91	H-Bond (Protein Donor)	false
N6	OD1	ASP- 89	2.98	156.72	H-Bond (Ligand Donor)	false
N1	N	PHE- 90	3.16	172.37	H-Bond (Protein Donor)	false
N	O	ASN- 105	2.8	176.84	H-Bond (Ligand Donor)	false
SD	CB	PRO- 107	3.95	0	Hydrophobic	false