scPDB - 1njj entry

Protein Data Bank Entry:

PDB ID : 1njj

Resolution :2.450 Å

Experimental Method : X-ray

Deposition Date : 2002-12-31

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Ornithine decarboxylase
ID:	Q9TZZ6_TRYBG
AC:	Q9TZZ6
Organism:	Trypanosoma brucei gambiense
Reign:	Eukaryota
TaxID:	31285
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	82 %
D	18 %

Ligand binding site composition:

B-Factor:	36.708
Number of residues:	37
Including
Standard Amino Acids:	33
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.704	1066.500

% Hydrophobic	% Polar
30.06	69.94
According to VolSite

Ligand :

HET Code:	ORX
Formula:	C13H21N3O7P
Molecular weight:	362.296 g/mol
DrugBank ID:	-
Buried Surface Area:	68.95 %
Polar Surface area:	199.73 Å2

Number of
H-Bond Acceptors:	8
H-Bond Donors:	3
Rings:	1
Aromatic rings:	1
Anionic atoms:	3
Cationic atoms:	2
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
9.03621	5.46729	30.2079

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
C5A	CB	ALA- 67	3.85	0	Hydrophobic	false
N1	NZ	LYS- 69	3.46	156.59	H-Bond (Protein Donor)	false
C4	CD	LYS- 69	3.98	0	Hydrophobic	false
OP2	N	GLY- 237	2.79	143.78	H-Bond (Protein Donor)	false
OP2	N	GLY- 276	3.03	131.33	H-Bond (Protein Donor)	false
OP3	N	ARG- 277	3.08	160.56	H-Bond (Protein Donor)	false
OP3	CZ	ARG- 277	3.72	0	Ionic (Protein Cationic)	false
NE	OD2	ASP- 332	3.33	160.46	H-Bond (Ligand Donor)	false
NE	OD2	ASP- 332	3.33	0	Ionic (Ligand Cationic)	false
C3	CB	CYS- 360	4.08	0	Hydrophobic	false
C2A	SG	CYS- 360	4.27	0	Hydrophobic	false
NE	OD2	ASP- 361	3.43	131.63	H-Bond (Ligand Donor)	false
NE	OD2	ASP- 361	3.43	0	Ionic (Ligand Cationic)	false
OP4	OH	TYR- 389	2.84	131.21	H-Bond (Protein Donor)	false
OP3	OH	TYR- 389	3.34	154.33	H-Bond (Protein Donor)	false
CBA	CZ	TYR- 389	4.35	0	Hydrophobic	false
O3	O	HOH- 467	2.79	179.96	H-Bond (Protein Donor)	false
OP2	O	HOH- 620	3.34	139.41	H-Bond (Protein Donor)	false