scPDB - 5c3c entry

Protein Data Bank Entry:

PDB ID : 5c3c

Resolution :2.800 Å

Experimental Method : X-ray

Deposition Date : 2015-06-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	CbbQ/NirQ/NorQ domain protein
ID:	D0KZ75_HALNC
AC:	D0KZ75
Organism:	Halothiobacillus neapolitanus
Reign:	Bacteria
TaxID:	555778
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	63.732
Number of residues:	29
Including
Standard Amino Acids:	29
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.666	448.875

% Hydrophobic	% Polar
59.40	40.60
According to VolSite

Ligand :

HET Code:	ADP
Formula:	C10H12N5O10P2
Molecular weight:	424.177 g/mol
DrugBank ID:	-
Buried Surface Area:	68.99 %
Polar Surface area:	260.7 Å2

Number of
H-Bond Acceptors:	14
H-Bond Donors:	3
Rings:	3
Aromatic rings:	2
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
230.835	173.969	1.08926

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
N6	O	ARG- 17	2.8	139.59	H-Bond (Ligand Donor)	false
O1B	N	GLY- 43	2.53	153.21	H-Bond (Protein Donor)	false
O3B	N	CYS- 44	2.79	129.01	H-Bond (Protein Donor)	false
O3B	N	GLY- 45	2.65	147	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 46	3.45	154.96	H-Bond (Protein Donor)	false
O3B	N	LYS- 46	3.01	138.73	H-Bond (Protein Donor)	false
O2B	NZ	LYS- 46	3.45	0	Ionic (Protein Cationic)	false
O2B	OG	SER- 47	2.68	155.74	H-Bond (Protein Donor)	false
O2B	N	SER- 47	2.86	141.63	H-Bond (Protein Donor)	false
C2'	CD	ARG- 48	4.42	0	Hydrophobic	false
C1'	CG2	ILE- 185	4.22	0	Hydrophobic	false
C2'	CG	GLU- 189	4.44	0	Hydrophobic	false
C1'	CG2	THR- 221	4.33	0	Hydrophobic	false
C4'	CB	ARG- 222	4.4	0	Hydrophobic	false