scPDB - 3w2j entry

Protein Data Bank Entry:

PDB ID : 3w2j

Resolution :1.420 Å

Experimental Method : X-ray

Deposition Date : 2012-11-28

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
B	100 %

Ligand binding site composition:

B-Factor:	10.905
Number of residues:	27
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	FMN
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.479	610.875

% Hydrophobic	% Polar
32.60	67.40
According to VolSite

Ligand :

HET Code:	QRO
Formula:	C13H9F2N2O4
Molecular weight:	295.218 g/mol
DrugBank ID:	-
Buried Surface Area:	69.12 %
Polar Surface area:	98.33 Å2

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

Mass center Coordinates

X	Y	Z
-4.96929	-12.9813	12.723

Binding mode :

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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
OAA	NZ	LYS- 43	3.06	148.11	H-Bond (Protein Donor)	false
OAA	NZ	LYS- 43	3.06	0	Ionic (Protein Cationic)	false
NAL	OD1	ASN- 67	2.9	171.73	H-Bond (Ligand Donor)	false
OAB	ND2	ASN- 67	2.92	171.71	H-Bond (Protein Donor)	false
OAD	N	GLY- 70	3.15	143.74	H-Bond (Protein Donor)	false
OAA	N	LEU- 71	2.9	145.79	H-Bond (Protein Donor)	false
CAG	CB	LEU- 71	4.3	0	Hydrophobic	false
CAK	CD1	LEU- 71	3.84	0	Hydrophobic	false
OAC	ND2	ASN- 127	2.96	161.02	H-Bond (Protein Donor)	false
CAI	CB	SER- 129	4.26	0	Hydrophobic	false
CAH	CG	PRO- 131	3.74	0	Hydrophobic	false
NAM	OD1	ASN- 194	2.81	174.71	H-Bond (Ligand Donor)	false
OAC	ND2	ASN- 194	2.93	155.34	H-Bond (Protein Donor)	false
OAB	OG	SER- 195	2.73	143.35	H-Bond (Protein Donor)	false
FAE	CD	LYS- 214	4.23	0	Hydrophobic	false