scPDB - 2nu9 entry

Protein Data Bank Entry:

PDB ID : 2nu9

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2006-11-08

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-forming] subunit alpha
ID:	SUCD_ECOLI
AC:	P0AGE9
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	6.2.1.5

Chains:

Chain Name:	Percentage of Residues within binding site
A	80 %
E	16 %
G	4 %

Ligand binding site composition:

B-Factor:	31.037
Number of residues:	51
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.258	904.500

% Hydrophobic	% Polar
53.36	46.64
According to VolSite

Ligand :

HET Code:	COA
Formula:	C21H32N7O16P3S
Molecular weight:	763.502 g/mol
DrugBank ID:	DB01992
Buried Surface Area:	60.64 %
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
44.5912	36.9347	133.929

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
O1A	N	SER- 18	3	170.06	H-Bond (Protein Donor)	false
O1A	OG	SER- 18	3.46	141.05	H-Bond (Protein Donor)	false
O4A	N	GLN- 19	3.17	155.4	H-Bond (Protein Donor)	false
CDP	CG	GLN- 19	3.39	0	Hydrophobic	false
OAP	OE2	GLU- 33	3.2	155.2	H-Bond (Ligand Donor)	false
C3B	CB	SER- 36	4.11	0	Hydrophobic	false
O2A	OG	SER- 36	3.15	152.18	H-Bond (Protein Donor)	false
C2B	CG2	THR- 39	4.28	0	Hydrophobic	false
O7A	NZ	LYS- 42	3.06	166.3	H-Bond (Protein Donor)	false
O7A	NZ	LYS- 42	3.06	0	Ionic (Protein Cationic)	false
O9A	NZ	LYS- 42	3.8	0	Ionic (Protein Cationic)	false
O9A	NZ	LYS- 66	3.6	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 66	2.74	0	Ionic (Protein Cationic)	false
O2A	NZ	LYS- 66	3.81	0	Ionic (Protein Cationic)	false
O1A	NZ	LYS- 66	2.74	161.71	H-Bond (Protein Donor)	false
C5B	CG	PRO- 73	4.41	0	Hydrophobic	false
CCP	CB	PRO- 73	4.44	0	Hydrophobic	false
C6P	CG2	ILE- 95	4.37	0	Hydrophobic	false
N4P	O	ILE- 95	3.06	153.51	H-Bond (Ligand Donor)	false
CEP	CG2	THR- 96	4.02	0	Hydrophobic	false
O9P	N	GLU- 97	2.8	166.8	H-Bond (Protein Donor)	false
C6P	CB	GLU- 97	4.39	0	Hydrophobic	false
S1P	CB	PRO- 124	3.87	0	Hydrophobic	false
C2P	CD1	ILE- 136	3.36	0	Hydrophobic	false