scPDB - 1nen entry

Protein Data Bank Entry:

PDB ID : 1nen

Resolution :2.900 Å

Experimental Method : X-ray

Deposition Date : 2002-12-11

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Succinate dehydrogenase iron-sulfur subunit	Succinate dehydrogenase cytochrome b556 subunit
ID:	SDHB_ECOLI	DHSC_ECOLI
AC:	P07014	P69054
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	1.3.5.1	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	36 %
C	55 %
D	9 %

Ligand binding site composition:

B-Factor:	58.622
Number of residues:	23
Including
Standard Amino Acids:	21
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.102	324.000

% Hydrophobic	% Polar
73.96	26.04
According to VolSite

Ligand :

HET Code:	DNT
Formula:	C13H17N2O5
Molecular weight:	281.284 g/mol
DrugBank ID:	DB07671
Buried Surface Area:	57.99 %
Polar Surface area:	114.69 Å2

Number of
H-Bond Acceptors:	5
H-Bond Donors:	0
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
86.6147	95.7255	106.577

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
C10	CD1	LEU- 15	3.36	0	Hydrophobic	false
C10	CZ	PHE- 20	4.47	0	Hydrophobic	false
C3	CB	ILE- 28	4.27	0	Hydrophobic	false
C5	CB	ILE- 28	4.47	0	Hydrophobic	false
C12	CD1	ILE- 28	3.35	0	Hydrophobic	false
O62	CZ	ARG- 31	3.77	0	Ionic (Protein Cationic)	false
C13	CG2	VAL- 32	4.02	0	Hydrophobic	false
C3	CB	PRO- 160	3.65	0	Hydrophobic	false
C5	CG	PRO- 160	3.63	0	Hydrophobic	false
C1	CB	PRO- 160	3.77	0	Hydrophobic	false
C10	CZ3	TRP- 163	3.54	0	Hydrophobic	false
C10	CZ2	TRP- 164	3.79	0	Hydrophobic	false
O1	NE1	TRP- 164	3.19	147.21	H-Bond (Protein Donor)	false
O62	NE1	TRP- 164	3.49	146.2	H-Bond (Protein Donor)	false
C3	CD1	ILE- 209	3.62	0	Hydrophobic	false