scPDB - 4r81 entry

Protein Data Bank Entry:

PDB ID : 4r81

Resolution :1.500 Å

Experimental Method : X-ray

Deposition Date : 2014-08-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Predicted NADH dehydrogenase
ID:	D9PVS9_METTM
AC:	D9PVS9
Organism:	Methanothermobacter marburgensis
Reign:	Archaea
TaxID:	79929
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	71 %
B	29 %

Ligand binding site composition:

B-Factor:	22.656
Number of residues:	36
Including
Standard Amino Acids:	35
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.080	1093.500

% Hydrophobic	% Polar
40.43	59.57
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	67.15 %
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
11.1559	59.7793	28.9318

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
O3P	NE2	HIS- 9	2.78	154.13	H-Bond (Protein Donor)	false
O1P	N	PHE- 15	2.9	155.37	H-Bond (Protein Donor)	false
O2P	OG	SER- 16	2.71	145.98	H-Bond (Protein Donor)	false
O2P	N	SER- 16	2.7	148.9	H-Bond (Protein Donor)	false
C7M	CD2	LEU- 48	4.32	0	Hydrophobic	false
O1P	OH	TYR- 53	2.94	124.61	H-Bond (Protein Donor)	false
O3P	OH	TYR- 53	3.06	131.79	H-Bond (Protein Donor)	false
C8M	CB	GLU- 56	4.11	0	Hydrophobic	false
C8M	CD1	ILE- 57	4.42	0	Hydrophobic	false
C4'	CB	PRO- 87	3.98	0	Hydrophobic	false
O2'	O	LEU- 88	2.9	163.45	H-Bond (Ligand Donor)	false
C7M	CD2	TRP- 89	4.27	0	Hydrophobic	false
C8M	CE2	TRP- 89	4.42	0	Hydrophobic	false
C6	CB	TRP- 89	3.73	0	Hydrophobic	false
N5	N	TRP- 90	2.96	160.5	H-Bond (Protein Donor)	false
O4	N	SER- 91	3.05	133.13	H-Bond (Protein Donor)	false
O4'	O	SER- 132	2.97	121.92	H-Bond (Ligand Donor)	false
O4'	OG	SER- 132	2.67	162.02	H-Bond (Protein Donor)	false
O5'	OG	SER- 132	3.3	120.95	H-Bond (Protein Donor)	false
N1	N	GLY- 134	3.13	148.2	H-Bond (Protein Donor)	false
O2'	N	GLY- 134	3.31	126.11	H-Bond (Protein Donor)	false
O2	N	HIS- 135	2.82	167.2	H-Bond (Protein Donor)	false
C5'	CB	MET- 174	4.19	0	Hydrophobic	false