scPDB - 4kcf entry

Protein Data Bank Entry:

PDB ID : 4kcf

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2013-04-24

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	FAD-dependent oxidoreductase
ID:	B3TMR1_9ACTN
AC:	B3TMR1
Organism:	Actinomadura kijaniata
Reign:	Bacteria
TaxID:	46161
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	31.898
Number of residues:	47
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	1
Water Molecules:	5
Cofactors:	FMN
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.089	1134.000

% Hydrophobic	% Polar
44.05	55.95
According to VolSite

Ligand :

HET Code:	AKM
Formula:	C17H28N3O14P2
Molecular weight:	560.363 g/mol
DrugBank ID:	-
Buried Surface Area:	66.33 %
Polar Surface area:	283.77 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	5
Rings:	3
Aromatic rings:	0
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
17.6959	24.0081	-16.2532

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
C6	SD	MET- 102	3.94	0	Hydrophobic	false
C4	SD	MET- 102	3.86	0	Hydrophobic	false
C6	CB	SER- 105	3.7	0	Hydrophobic	false
O3P	CZ	ARG- 106	3.53	0	Ionic (Protein Cationic)	false
O3P	NH2	ARG- 106	2.86	158.71	H-Bond (Protein Donor)	false
O3P	NH1	ARG- 106	3.37	131.98	H-Bond (Protein Donor)	false
C1'	CB	THR- 109	3.79	0	Hydrophobic	false
C2'	CD2	TYR- 112	4.17	0	Hydrophobic	false
C1'	CB	TYR- 112	4.33	0	Hydrophobic	false
C5A	CE2	TYR- 112	4.11	0	Hydrophobic	false
O3'	OE1	GLU- 113	2.78	148.81	H-Bond (Ligand Donor)	false
C2'	CG	GLU- 113	4.18	0	Hydrophobic	false
O4A	OG	SER- 141	3.02	145.02	H-Bond (Protein Donor)	false
C6	CB	SER- 141	4.23	0	Hydrophobic	false
C5	CB	SER- 141	3.58	0	Hydrophobic	false
C1	CD1	ILE- 143	4.43	0	Hydrophobic	false
C2	CG1	ILE- 143	3.5	0	Hydrophobic	false
O3'	NH2	ARG- 240	3.35	135.17	H-Bond (Protein Donor)	false
C5A	CB	ALA- 252	4.42	0	Hydrophobic	false
O2P	OG	SER- 257	2.64	156.31	H-Bond (Protein Donor)	false
C1	CB	SER- 257	3.96	0	Hydrophobic	false
C3M	CB	SER- 258	4.12	0	Hydrophobic	false
O41	NH1	ARG- 330	2.92	136.04	H-Bond (Protein Donor)	false
O41	NH2	ARG- 330	2.65	150.73	H-Bond (Protein Donor)	false
N3	O2	FMN- 502	3.28	147.91	H-Bond (Ligand Donor)	false
O3'	O	HOH- 622	3.11	179.97	H-Bond (Protein Donor)	false