scPDB - 4kto entry

Protein Data Bank Entry:

PDB ID : 4kto

Resolution :2.140 Å

Experimental Method : X-ray

Deposition Date : 2013-05-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Putative isovaleryl-CoA dehydrogenase protein
ID:	Q92VK1_RHIME
AC:	Q92VK1
Organism:	Rhizobium meliloti
Reign:	Bacteria
TaxID:	266834
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	68 %
C	32 %

Ligand binding site composition:

B-Factor:	33.357
Number of residues:	52
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.579	1913.625

% Hydrophobic	% Polar
49.03	50.97
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	56.14 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
78.3695	72.9129	105.353

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
C7M	CD2	LEU- 90	3.56	0	Hydrophobic	false
N3	O	LEU- 128	2.62	135.77	H-Bond (Ligand Donor)	false
O2	N	MET- 130	2.54	137.52	H-Bond (Protein Donor)	false
N1	OG	SER- 131	2.86	151.57	H-Bond (Protein Donor)	false
O2	OG	SER- 131	3.37	144.83	H-Bond (Protein Donor)	false
O2	N	SER- 131	2.8	154.8	H-Bond (Protein Donor)	false
C1'	CB	SER- 131	3.67	0	Hydrophobic	false
C7M	CE3	TRP- 161	4.33	0	Hydrophobic	false
C8M	CD2	TRP- 161	3.94	0	Hydrophobic	false
C1'	CB	TRP- 161	3.56	0	Hydrophobic	false
C9A	CB	TRP- 161	3.54	0	Hydrophobic	false
C6	CB	THR- 163	4.27	0	Hydrophobic	false
C1B	CE	MET- 286	3.39	0	Hydrophobic	false
O3B	O	GLN- 341	2.52	153.95	H-Bond (Ligand Donor)	false
O2P	N	GLY- 345	3	141.32	H-Bond (Protein Donor)	false
C8M	CD2	LEU- 363	3.24	0	Hydrophobic	false
C7M	CD2	LEU- 363	3.26	0	Hydrophobic	false
C5'	CG2	ILE- 366	3.76	0	Hydrophobic	false
O2'	N	GLY- 369	3.4	166.68	H-Bond (Protein Donor)	false
C2B	CG2	THR- 370	4.37	0	Hydrophobic	false
C5'	CG2	THR- 370	3.7	0	Hydrophobic	false
O2B	OG1	THR- 370	3.2	161.03	H-Bond (Protein Donor)	false
C2B	CB	GLU- 372	4.34	0	Hydrophobic	false
O4	O	HOH- 668	2.69	166.66	H-Bond (Protein Donor)	false