scPDB - 4kpu entry

Protein Data Bank Entry:

PDB ID : 4kpu

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2013-05-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Electron transfer flavoprotein alpha/beta-subunit
ID:	D2RIQ2_ACIFV
AC:	D2RIQ2
Organism:	Acidaminococcus fermentans
Reign:	Bacteria
TaxID:	591001
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	23 %
B	77 %

Ligand binding site composition:

B-Factor:	9.851
Number of residues:	57
Including
Standard Amino Acids:	57
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.637	334.125

% Hydrophobic	% Polar
52.53	47.47
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	72.55 %
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
85.7789	55.8562	20.4011

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
O2B	O	CYS- 6	2.68	175.45	H-Bond (Ligand Donor)	false
C1B	CB	CYS- 6	4.1	0	Hydrophobic	false
O2P	NZ	LYS- 8	2.77	144.81	H-Bond (Protein Donor)	false
O2P	NZ	LYS- 8	2.77	0	Ionic (Protein Cationic)	false
O3B	OD1	ASP- 38	2.52	156.75	H-Bond (Ligand Donor)	false
N6A	O	MET- 61	2.88	172.38	H-Bond (Ligand Donor)	false
N1A	N	MET- 61	3.16	161.38	H-Bond (Protein Donor)	false
O3'	O	ALA- 92	2.67	148.45	H-Bond (Ligand Donor)	false
O2	N	THR- 94	2.88	165.97	H-Bond (Protein Donor)	false
C2'	CG2	THR- 94	4.4	0	Hydrophobic	false
C5'	CG2	THR- 94	3.92	0	Hydrophobic	false
O3'	OG1	THR- 97	3.16	149.56	H-Bond (Protein Donor)	false
O4'	OG1	THR- 97	2.85	162.02	H-Bond (Ligand Donor)	false
C5'	CG2	THR- 97	4.22	0	Hydrophobic	false
C4B	CB	CYS- 116	4.24	0	Hydrophobic	false
C2B	CB	CYS- 116	4.48	0	Hydrophobic	false
O2B	N	GLY- 117	2.99	149.27	H-Bond (Protein Donor)	false
O1A	N	ALA- 120	2.77	168.13	H-Bond (Protein Donor)	false
O1P	OG1	THR- 125	2.71	152.8	H-Bond (Protein Donor)	false
O1P	N	THR- 125	3	152.57	H-Bond (Protein Donor)	false
O1A	N	ALA- 126	2.85	146.09	H-Bond (Protein Donor)	false
N3	O	LEU- 127	2.96	171.95	H-Bond (Ligand Donor)	false
O2A	N	GLN- 127	2.99	133.74	H-Bond (Protein Donor)	false
O2A	N	VAL- 128	2.82	165.19	H-Bond (Protein Donor)	false
C1B	CG1	VAL- 128	3.95	0	Hydrophobic	false
C5'	CG2	VAL- 128	3.63	0	Hydrophobic	false
C5B	CB	VAL- 128	4.08	0	Hydrophobic	false
O4	N	ALA- 129	3.35	153.22	H-Bond (Protein Donor)	false
N5	NH1	ARG- 146	2.86	129.22	H-Bond (Protein Donor)	false
C7M	CB	ALA- 148	3.65	0	Hydrophobic	false
C7M	CG2	ILE- 153	4.13	0	Hydrophobic	false
C7M	CB	ALA- 155	3.95	0	Hydrophobic	false
C6	CD1	ILE- 157	4.46	0	Hydrophobic	false
C8	CG2	VAL- 223	4.08	0	Hydrophobic	false