scPDB - 2ptf entry

Protein Data Bank Entry:

PDB ID : 2ptf

Resolution :2.350 Å

Experimental Method : X-ray

Deposition Date : 2007-05-08

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Uncharacterized protein MTH_863
ID:	Y863_METTH
AC:	O26951
Organism:	Methanothermobacter thermautotrophicus
Reign:	Archaea
TaxID:	187420
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	88 %
B	12 %

Ligand binding site composition:

B-Factor:	35.855
Number of residues:	36
Including
Standard Amino Acids:	34
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.838	901.125

% Hydrophobic	% Polar
49.81	50.19
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	56.45 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
18.1576	36.5492	19.9431

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
O2P	ND2	ASN- 48	3.46	133.16	H-Bond (Protein Donor)	false
O3P	ND2	ASN- 48	2.78	160.78	H-Bond (Protein Donor)	false
C5'	CB	ALA- 50	3.87	0	Hydrophobic	false
O2'	O	PRO- 51	2.78	163.65	H-Bond (Ligand Donor)	false
C7	CB	PRO- 51	3.8	0	Hydrophobic	false
C8	CB	PRO- 51	3.7	0	Hydrophobic	false
C8	CB	PRO- 51	3.7	0	Hydrophobic	false
O4	N	GLY- 53	3.01	154.91	H-Bond (Protein Donor)	false
N3	O	TYR- 65	2.68	164.88	H-Bond (Ligand Donor)	false
O2	N	TYR- 67	2.83	166.63	H-Bond (Protein Donor)	false
C5'	CG2	THR- 70	4.4	0	Hydrophobic	false
O1P	N	ARG- 71	3.1	159.8	H-Bond (Protein Donor)	false
O3P	NH2	ARG- 71	3.12	121.47	H-Bond (Protein Donor)	false
O3P	CZ	ARG- 71	3.7	0	Ionic (Protein Cationic)	false
O2P	OG1	THR- 72	2.51	157.36	H-Bond (Protein Donor)	false
O2P	N	THR- 72	2.98	149	H-Bond (Protein Donor)	false
C8M	CG2	THR- 97	4.17	0	Hydrophobic	false
C7M	CG2	ILE- 171	4.04	0	Hydrophobic	false
C8M	CB	LEU- 174	3.56	0	Hydrophobic	false
C7	CG1	ILE- 175	3.96	0	Hydrophobic	false
C8M	CG2	THR- 178	4.23	0	Hydrophobic	false
C9	CG2	THR- 178	4.23	0	Hydrophobic	false
C1'	CG2	THR- 178	4.41	0	Hydrophobic	false
O4	O	HOH- 302	2.71	157.92	H-Bond (Protein Donor)	false