scPDB - 4yxd entry

Protein Data Bank Entry:

PDB ID : 4yxd

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2015-03-23

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial
ID:	SDHA_PIG
AC:	Q0QF01
Organism:	Sus scrofa
Reign:	Eukaryota
TaxID:	9823
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
A	99 %
B	1 %

Ligand binding site composition:

B-Factor:	76.456
Number of residues:	77
Including
Standard Amino Acids:	77
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.516	344.250

% Hydrophobic	% Polar
46.08	53.92
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	81.27 %
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
-11.7277	-13.8054	22.4739

Binding mode :

What is Poseview ?

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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
O3B	N	ALA- 27	2.58	154.21	H-Bond (Protein Donor)	false
O2B	OG1	THR- 49	2.88	145.64	H-Bond (Ligand Donor)	false
C2B	CG	LYS- 50	4.35	0	Hydrophobic	false
N3A	N	LYS- 50	3.06	143.45	H-Bond (Protein Donor)	false
O2B	N	LEU- 51	3.31	135.77	H-Bond (Protein Donor)	false
C3B	CB	SER- 56	3.8	0	Hydrophobic	false
O3B	OG	SER- 56	2.58	148.59	H-Bond (Ligand Donor)	false
O1A	N	THR- 58	3	125.78	H-Bond (Protein Donor)	false
C4'	CG2	THR- 58	3.77	0	Hydrophobic	false
C7M	CB	ALA- 60	4.2	0	Hydrophobic	false
C9A	CB	ALA- 61	4.38	0	Hydrophobic	false
O4	N	GLY- 63	2.62	125.33	H-Bond (Protein Donor)	false
N3	O	GLY- 64	3.23	148.05	H-Bond (Ligand Donor)	false
O4	N	GLY- 64	3.31	142.34	H-Bond (Protein Donor)	false
N6A	O	ALA- 179	3.39	157.42	H-Bond (Ligand Donor)	false
N1A	N	ALA- 179	2.87	171.8	H-Bond (Protein Donor)	false
C7M	CB	THR- 225	4.36	0	Hydrophobic	false
C8M	CB	THR- 225	3.91	0	Hydrophobic	false
N6A	OD1	ASP- 233	3.09	153.17	H-Bond (Ligand Donor)	false
C6	CD2	LEU- 264	3.78	0	Hydrophobic	false
C7	CD1	LEU- 264	4.03	0	Hydrophobic	false
C7M	CB	LEU- 264	3.44	0	Hydrophobic	false
C1'	CD1	TYR- 366	4.01	0	Hydrophobic	false
C3'	CE1	TYR- 366	4.43	0	Hydrophobic	false
C5'	CB	GLU- 398	4.03	0	Hydrophobic	false
O2P	N	GLU- 398	3.14	135.83	H-Bond (Protein Donor)	false
O3'	OG	SER- 414	2.95	148.58	H-Bond (Protein Donor)	false
C2'	CB	SER- 414	3.88	0	Hydrophobic	false
O2	N	LEU- 415	2.69	163.71	H-Bond (Protein Donor)	false
C4'	CD2	LEU- 418	3.61	0	Hydrophobic	false
C5'	CD1	LEU- 418	3.8	0	Hydrophobic	false