scPDB - 1ep3 entry

Protein Data Bank Entry:

PDB ID : 1ep3

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2000-03-27

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit
ID:	PYRDB_LACLM
AC:	P54322
Organism:	Lactococcus lactis subsp. cremoris
Reign:	Bacteria
TaxID:	416870
EC Number:	1.3.1.14

Chains:

Chain Name:	Percentage of Residues within binding site
A	96 %
B	4 %

Ligand binding site composition:

B-Factor:	16.111
Number of residues:	50
Including
Standard Amino Acids:	46
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.084	857.250

% Hydrophobic	% Polar
40.94	59.06
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	77.89 %
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
7.2129	167.135	27.0326

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
C2'	CB	ALA- 23	4.23	0	Hydrophobic	false
O2'	O	SER- 24	2.81	160.97	H-Bond (Ligand Donor)	false
C8M	SG	CYS- 26	4.02	0	Hydrophobic	false
O4	N	ALA- 49	3.2	152.18	H-Bond (Protein Donor)	false
C8M	SD	MET- 70	4.39	0	Hydrophobic	false
C7M	CB	ASN- 72	3.93	0	Hydrophobic	false
C8M	CB	ASN- 72	4.32	0	Hydrophobic	false
C7M	CG1	ILE- 74	3.97	0	Hydrophobic	false
O2	ND2	ASN- 104	2.75	135.02	H-Bond (Protein Donor)	false
N3	OD1	ASN- 104	2.93	161.73	H-Bond (Ligand Donor)	false
O3'	NZ	LYS- 170	2.89	162.41	H-Bond (Protein Donor)	false
O3'	O	ILE- 196	2.91	154.24	H-Bond (Ligand Donor)	false
C4'	CG2	THR- 198	3.8	0	Hydrophobic	false
C8M	CB	SER- 221	4.19	0	Hydrophobic	false
C4'	CB	SER- 221	4.23	0	Hydrophobic	false
O3P	N	GLY- 222	2.86	155.38	H-Bond (Protein Donor)	false
C5'	CD1	ILE- 225	4.18	0	Hydrophobic	false
C7M	CB	CYS- 231	4.48	0	Hydrophobic	false
C3'	SD	MET- 247	3.93	0	Hydrophobic	false
C5'	CG	MET- 247	4.33	0	Hydrophobic	false
O1P	N	GLY- 249	3.49	137.37	H-Bond (Protein Donor)	false
O3P	N	GLY- 249	2.62	157.09	H-Bond (Protein Donor)	false
O1P	N	GLY- 270	3.01	147.46	H-Bond (Protein Donor)	false
O1P	N	THR- 271	3.49	125.11	H-Bond (Protein Donor)	false
O2P	N	THR- 271	2.8	172.26	H-Bond (Protein Donor)	false
O2P	OG1	THR- 271	2.74	159.65	H-Bond (Protein Donor)	false
C7M	CZ	PHE- 274	4.01	0	Hydrophobic	false
C8M	CE2	PHE- 274	4.34	0	Hydrophobic	false
O1P	O	HOH- 505	2.65	179.94	H-Bond (Protein Donor)	false
O1P	O	HOH- 520	2.6	179.95	H-Bond (Protein Donor)	false