scPDB - 2djl entry

Protein Data Bank Entry:

PDB ID : 2djl

Resolution :1.380 Å

Experimental Method : X-ray

Deposition Date : 2006-04-04

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydroorotate dehydrogenase (fumarate)
ID:	PYRD_TRYCC
AC:	Q4D3W2
Organism:	Trypanosoma cruzi
Reign:	Eukaryota
TaxID:	353153
EC Number:	1.3.98.1

Chains:

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

Ligand binding site composition:

B-Factor:	8.095
Number of residues:	50
Including
Standard Amino Acids:	50
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.596	631.125

% Hydrophobic	% Polar
35.83	64.17
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	75.21 %
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
8.85774	46.9984	78.5507

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- 18	3.81	0	Hydrophobic	false
O2'	O	ALA- 19	2.84	161.16	H-Bond (Ligand Donor)	false
C8	CG2	VAL- 21	4.24	0	Hydrophobic	false
O4	NZ	LYS- 43	2.84	147.18	H-Bond (Protein Donor)	false
N5	NZ	LYS- 43	3.15	134.3	H-Bond (Protein Donor)	false
N3	OG	SER- 44	2.72	170.07	H-Bond (Ligand Donor)	false
O4	N	SER- 44	3.3	145.45	H-Bond (Protein Donor)	false
C7M	CD2	TYR- 58	3.86	0	Hydrophobic	false
C8M	CE2	TYR- 58	3.88	0	Hydrophobic	false
C7M	CB	ASN- 67	4.43	0	Hydrophobic	false
C7M	CG	MET- 69	3.79	0	Hydrophobic	false
O2	NZ	LYS- 164	2.98	159.08	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 164	2.84	140.48	H-Bond (Protein Donor)	false
O3'	NZ	LYS- 164	3.18	140.7	H-Bond (Protein Donor)	false
O3'	O	VAL- 193	2.9	141.07	H-Bond (Ligand Donor)	false
O1P	N	GLY- 222	2.73	162.72	H-Bond (Protein Donor)	false
C5'	CD1	ILE- 225	3.73	0	Hydrophobic	false
C3'	SG	CYS- 248	3.52	0	Hydrophobic	false
O1P	N	GLY- 250	2.77	164.9	H-Bond (Protein Donor)	false
O2P	N	GLY- 271	2.9	141.35	H-Bond (Protein Donor)	false
O2P	N	THR- 272	3.4	129.67	H-Bond (Protein Donor)	false
O3P	OG1	THR- 272	2.71	160.05	H-Bond (Protein Donor)	false
O3P	N	THR- 272	2.77	165.31	H-Bond (Protein Donor)	false