scPDB - 5cae entry

Protein Data Bank Entry:

PDB ID : 5cae

Resolution :2.200 Å

Experimental Method : X-ray

Deposition Date : 2015-06-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
ID:	SUCA_PIG
AC:	O19069
Organism:	Sus scrofa
Reign:	Eukaryota
TaxID:	9823
EC Number:	6.2.1.4

Chains:

Chain Name:	Percentage of Residues within binding site
A	88 %
B	12 %

Ligand binding site composition:

B-Factor:	23.662
Number of residues:	53
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	MG

Cavity properties

Ligandability	Volume (Å3)
0.735	459.000

% Hydrophobic	% Polar
47.79	52.21
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	54.63 %
Polar Surface area:	426.11 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	6
Rings:	3
Aromatic rings:	2
Anionic atoms:	4
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	18

Mass center Coordinates

X	Y	Z
18.3945	6.08862	29.3658

Binding mode :

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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
O8A	OG1	THR- 24	2.52	172.82	H-Bond (Protein Donor)	false
O2A	N	LYS- 26	2.91	167.47	H-Bond (Protein Donor)	false
O4A	N	GLN- 27	2.79	167.28	H-Bond (Protein Donor)	false
CEP	CG	GLN- 27	3.69	0	Hydrophobic	false
C1B	CG2	THR- 47	4.19	0	Hydrophobic	false
O8A	NZ	LYS- 50	2.64	170.75	H-Bond (Protein Donor)	false
O8A	NZ	LYS- 50	2.64	0	Ionic (Protein Cationic)	false
O9A	NZ	LYS- 50	3.6	0	Ionic (Protein Cationic)	false
CEP	CD2	TYR- 79	4.49	0	Hydrophobic	false
C5B	CG	PRO- 81	3.69	0	Hydrophobic	false
C6P	CG2	ILE- 103	4.23	0	Hydrophobic	false
C2P	CG2	ILE- 103	4.28	0	Hydrophobic	false
N4P	O	ILE- 103	2.88	170.19	H-Bond (Ligand Donor)	false
CDP	CB	THR- 104	3.97	0	Hydrophobic	false
O9P	N	GLU- 105	2.85	153.05	H-Bond (Protein Donor)	false
C6P	CB	GLU- 105	4.24	0	Hydrophobic	false
S1P	CB	PRO- 133	4.03	0	Hydrophobic	false
C2P	CD1	ILE- 145	3.5	0	Hydrophobic	false
O4A	O	HOH- 552	2.76	179.96	H-Bond (Protein Donor)	false
N1A	O	HOH- 565	2.83	179.98	H-Bond (Protein Donor)	false