scPDB - 1d3g entry

Protein Data Bank Entry:

PDB ID : 1d3g

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 1999-09-29

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.100	8.100	8.100	0.000	8.100	1

List of CHEMBLId :

CHEMBL288708

Binding Site :

Uniprot Annotation

Name:	Dihydroorotate dehydrogenase (quinone), mitochondrial
ID:	PYRD_HUMAN
AC:	Q02127
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.3.5.2

Chains:

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

Ligand binding site composition:

B-Factor:	23.081
Number of residues:	39
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	1
Water Molecules:	1
Cofactors:	FMN
Metals:

Cavity properties

Ligandability	Volume (Å3)
2.001	560.250

% Hydrophobic	% Polar
77.71	22.29
According to VolSite

Ligand :

HET Code:	BRE
Formula:	C23H15FNO2
Molecular weight:	356.369 g/mol
DrugBank ID:	DB03480
Buried Surface Area:	71.23 %
Polar Surface area:	53.02 Å2

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

Mass center Coordinates

X	Y	Z
50.8266	43.2287	-2.52404

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
C1	CE	MET- 43	3.72	0	Hydrophobic	false
C19	SD	MET- 43	4.42	0	Hydrophobic	false
C23	CE	MET- 43	3.8	0	Hydrophobic	false
C1	CD2	LEU- 46	4.38	0	Hydrophobic	false
C12	CD2	LEU- 46	3.58	0	Hydrophobic	false
C1	CG	GLN- 47	3.9	0	Hydrophobic	false
O1	NE2	GLN- 47	3.07	158.75	H-Bond (Protein Donor)	false
C10	CB	PRO- 52	3.89	0	Hydrophobic	false
C2	CB	ALA- 55	3.8	0	Hydrophobic	false
C6	CB	HIS- 56	4.46	0	Hydrophobic	false
C11	CB	HIS- 56	3.47	0	Hydrophobic	false
C18	CB	ALA- 59	4.23	0	Hydrophobic	false
C12	CB	ALA- 59	3.55	0	Hydrophobic	false
C20	CB	PHE- 62	4.08	0	Hydrophobic	false
C20	CD2	LEU- 68	3.48	0	Hydrophobic	false
C20	CE	MET- 111	4.46	0	Hydrophobic	false
C14	CG1	VAL- 134	4.22	0	Hydrophobic	false
F1	CB	VAL- 134	4.46	0	Hydrophobic	false
O1	CZ	ARG- 136	3.74	0	Ionic (Protein Cationic)	false
O2	CZ	ARG- 136	3.47	0	Ionic (Protein Cationic)	false
O1	NE	ARG- 136	2.92	176.06	H-Bond (Protein Donor)	false
O2	NH2	ARG- 136	2.7	171.51	H-Bond (Protein Donor)	false
O2	NE	ARG- 136	3.46	130.67	H-Bond (Protein Donor)	false
F1	CG1	VAL- 143	3.99	0	Hydrophobic	false
C13	CG	LEU- 359	4.2	0	Hydrophobic	false
C4	CB	THR- 360	3.65	0	Hydrophobic	false
C11	CG2	THR- 360	3.55	0	Hydrophobic	false
C20	CG	PRO- 364	3.72	0	Hydrophobic	false
F1	C7M	FMN- 398	3.75	0	Hydrophobic	false