scPDB - 3oix entry

Protein Data Bank Entry:

PDB ID : 3oix

Resolution :2.400 Å

Experimental Method : X-ray

Deposition Date : 2010-08-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydroorotate dehydrogenase
ID:	Q8DVA1_STRMU
AC:	Q8DVA1
Organism:	Streptococcus mutans serotype c
Reign:	Bacteria
TaxID:	210007
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	24.101
Number of residues:	51
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	1
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.110	1117.125

% Hydrophobic	% Polar
35.95	64.05
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	73.26 %
Polar Surface area:	217.05 Å2

Number of
H-Bond Acceptors:	12
H-Bond Donors:	4
Rings:	3
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
17.4336	-25.5372	27.9234

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
C2'	CB	ALA- 20	3.84	0	Hydrophobic	false
C4'	CB	ALA- 20	4.14	0	Hydrophobic	false
O2'	O	ALA- 21	3.27	148.7	H-Bond (Ligand Donor)	false
C8	CG2	VAL- 23	3.83	0	Hydrophobic	false
N3	OG1	THR- 46	2.78	133.96	H-Bond (Ligand Donor)	false
C7M	CD2	TYR- 60	3.4	0	Hydrophobic	false
C8M	CE2	TYR- 60	3.83	0	Hydrophobic	false
C8M	CB	ASN- 69	4.46	0	Hydrophobic	false
C7M	CB	ASN- 69	3.89	0	Hydrophobic	false
C7M	CE	MET- 71	3.47	0	Hydrophobic	false
C6	CG	MET- 71	3.73	0	Hydrophobic	false
O2	NZ	LYS- 165	2.99	158.43	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 165	3	155.74	H-Bond (Protein Donor)	false
O4'	O	ILE- 193	2.59	155.59	H-Bond (Ligand Donor)	false
O1P	N	GLY- 220	2.64	166.36	H-Bond (Protein Donor)	false
C4'	CB	THR- 247	4.47	0	Hydrophobic	false
C5'	CG2	THR- 247	3.7	0	Hydrophobic	false
O1P	N	GLY- 249	2.84	171.56	H-Bond (Protein Donor)	false
O3P	N	GLY- 270	2.88	155.71	H-Bond (Protein Donor)	false
O2P	N	THR- 271	2.62	165.15	H-Bond (Protein Donor)	false
O2P	OG1	THR- 271	2.66	162.45	H-Bond (Protein Donor)	false
O3P	N	THR- 271	3.49	132.26	H-Bond (Protein Donor)	false
O3P	O	HOH- 312	2.58	159.14	H-Bond (Protein Donor)	false
O3P	O	HOH- 331	2.57	179.97	H-Bond (Protein Donor)	false