scPDB - 1dor entry

Protein Data Bank Entry:

PDB ID : 1dor

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 1997-01-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydroorotate dehydrogenase A (fumarate)
ID:	PYRDA_LACLM
AC:	A2RJT9
Organism:	Lactococcus lactis subsp. cremoris
Reign:	Bacteria
TaxID:	416870
EC Number:	1.3.98.1

Chains:

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

Ligand binding site composition:

B-Factor:	18.784
Number of residues:	54
Including
Standard Amino Acids:	49
Non Standard Amino Acids:	0
Water Molecules:	5
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.484	529.875

% Hydrophobic	% Polar
37.58	62.42
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	75.59 %
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
0.590355	17.5318	18.5649

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
C3'	CB	ALA- 18	4.08	0	Hydrophobic	false
C8M	CG2	VAL- 21	4.1	0	Hydrophobic	false
C8	CG2	VAL- 21	3.99	0	Hydrophobic	false
O4	NZ	LYS- 43	2.8	140.01	H-Bond (Protein Donor)	false
N5	NZ	LYS- 43	3.31	138.93	H-Bond (Protein Donor)	false
N3	OG	SER- 44	2.8	172.14	H-Bond (Ligand Donor)	false
C7M	CD2	TYR- 58	3.71	0	Hydrophobic	false
C8M	CE2	TYR- 58	3.95	0	Hydrophobic	false
C7M	CB	ASN- 67	4.34	0	Hydrophobic	false
C7M	CG	MET- 69	3.85	0	Hydrophobic	false
O2	NZ	LYS- 164	3.01	147.09	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 164	2.9	129.81	H-Bond (Protein Donor)	false
O3'	NZ	LYS- 164	3.17	144.98	H-Bond (Protein Donor)	false
O3'	O	VAL- 192	2.8	136.97	H-Bond (Ligand Donor)	false
O1P	N	GLY- 221	2.83	166.75	H-Bond (Protein Donor)	false
C5'	CD1	ILE- 224	3.79	0	Hydrophobic	false
C3'	CG2	THR- 248	3.59	0	Hydrophobic	false
O1P	N	GLY- 250	2.92	173.52	H-Bond (Protein Donor)	false
O3P	N	GLY- 271	2.95	143.73	H-Bond (Protein Donor)	false
O2P	N	THR- 272	2.88	160.12	H-Bond (Protein Donor)	false
O2P	OG1	THR- 272	2.76	161.3	H-Bond (Protein Donor)	false
O3P	N	THR- 272	3.35	135.23	H-Bond (Protein Donor)	false
O3P	O	HOH- 1001	2.74	160.4	H-Bond (Protein Donor)	false
O3P	O	HOH- 1018	2.71	156.91	H-Bond (Protein Donor)	false