scPDB - 3i68 entry

Protein Data Bank Entry:

PDB ID : 3i68

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2009-07-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydroorotate dehydrogenase (quinone), mitochondrial
ID:	PYRD_PLAF7
AC:	Q08210
Organism:	Plasmodium falciparum
Reign:	Eukaryota
TaxID:	36329
EC Number:	1.3.5.2

Chains:

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

Ligand binding site composition:

B-Factor:	54.243
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	FMN
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.515	337.500

% Hydrophobic	% Polar
70.00	30.00
According to VolSite

Ligand :

HET Code:	J4Z
Formula:	C20H15N5
Molecular weight:	325.367 g/mol
DrugBank ID:	DB08006
Buried Surface Area:	79.78 %
Polar Surface area:	55.11 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	1
Rings:	5
Aromatic rings:	5
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	0
Rotatable Bonds:	2

Mass center Coordinates

X	Y	Z
-22.4254	-18.7681	14.625

Binding mode :

What is Poseview ?

2D View
3D View

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
C14	CG	LEU- 172	3.97	0	Hydrophobic	false
C10	CD1	LEU- 172	3.73	0	Hydrophobic	false
C14	CB	CYS- 175	4.27	0	Hydrophobic	false
C14	CB	LEU- 176	4.08	0	Hydrophobic	false
C14	CB	CYS- 184	3.86	0	Hydrophobic	false
N1	ND1	HIS- 185	2.92	160.19	H-Bond (Ligand Donor)	false
C3	CB	HIS- 185	4.49	0	Hydrophobic	false
C9	CB	PHE- 188	4.13	0	Hydrophobic	false
C5	CB	PHE- 188	3.47	0	Hydrophobic	false
C5	CD2	LEU- 189	4.25	0	Hydrophobic	false
C22	CD2	LEU- 189	4.27	0	Hydrophobic	false
C24	CD1	LEU- 197	3.33	0	Hydrophobic	false
C4	CZ	PHE- 227	3.39	0	Hydrophobic	false
C23	SG	CYS- 233	3.62	0	Hydrophobic	false
C23	CB	SER- 236	4.21	0	Hydrophobic	false
C23	CG1	ILE- 237	3.48	0	Hydrophobic	false
C25	CD1	LEU- 240	3.52	0	Hydrophobic	false
N5	NH1	ARG- 265	2.95	139.95	H-Bond (Protein Donor)	false
C8	CD2	LEU- 531	4.27	0	Hydrophobic	false
C10	CB	LEU- 531	4.2	0	Hydrophobic	false
C1	CG2	VAL- 532	4.47	0	Hydrophobic	false
C8	CE	MET- 536	3.98	0	Hydrophobic	false
C25	SD	MET- 536	3.83	0	Hydrophobic	false