scPDB - 4xq6 entry

Protein Data Bank Entry:

PDB ID : 4xq6

Resolution :2.000 Å

Experimental Method : X-ray

Deposition Date : 2015-01-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydroorotate dehydrogenase (quinone)
ID:	PYRD_MYCTA
AC:	A5U4G5
Organism:	Mycobacterium tuberculosis
Reign:	Bacteria
TaxID:	419947
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	27.690
Number of residues:	48
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	1
Water Molecules:	3
Cofactors:
Metals:	CL

Cavity properties

Ligandability	Volume (Å3)
0.582	411.750

% Hydrophobic	% Polar
45.90	54.10
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	78.46 %
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
-4.70152	30.8978	53.843

Binding mode :

What is Poseview ?

2D View
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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- 65	4.07	0	Hydrophobic	false
O2'	O	ALA- 66	2.92	165.66	H-Bond (Ligand Donor)	false
N3	OG1	THR- 90	2.75	165.94	H-Bond (Ligand Donor)	false
O4	N	THR- 90	3.14	175.24	H-Bond (Protein Donor)	false
C7M	CD1	LEU- 104	3.71	0	Hydrophobic	false
C8M	CD1	LEU- 113	3.8	0	Hydrophobic	false
C7	CB	ASN- 115	3.96	0	Hydrophobic	false
O2	ND2	ASN- 143	2.99	120.11	H-Bond (Protein Donor)	false
N1	NZ	LYS- 212	3.01	135.22	H-Bond (Protein Donor)	false
O2	NZ	LYS- 212	2.96	149.84	H-Bond (Protein Donor)	false
O2'	NZ	LYS- 212	2.91	128.15	H-Bond (Protein Donor)	false
O3'	NZ	LYS- 212	3.09	152.55	H-Bond (Protein Donor)	false
O3'	O	THR- 240	2.92	140.55	H-Bond (Ligand Donor)	false
C9	CG2	THR- 242	4.15	0	Hydrophobic	false
C1'	CG2	THR- 242	4.11	0	Hydrophobic	false
C4'	CG2	THR- 242	3.96	0	Hydrophobic	false
C8M	CB	SER- 263	4.06	0	Hydrophobic	false
C4'	CB	SER- 263	4.2	0	Hydrophobic	false
O2P	N	GLY- 264	2.82	142.56	H-Bond (Protein Donor)	false
C5'	CD1	LEU- 267	3.34	0	Hydrophobic	false
C5'	CG2	VAL- 291	3.62	0	Hydrophobic	false
O2P	N	GLY- 293	2.72	154.98	H-Bond (Protein Donor)	false
C7M	CZ	TYR- 314	3.55	0	Hydrophobic	false
C8M	CE1	TYR- 314	4.02	0	Hydrophobic	false
C2'	CD2	TYR- 314	4.34	0	Hydrophobic	false
C7	CE2	TYR- 314	3.41	0	Hydrophobic	false
O3P	N	TYR- 314	2.95	172.58	H-Bond (Protein Donor)	false
O1P	N	THR- 315	2.89	158.45	H-Bond (Protein Donor)	false
O1P	OG1	THR- 315	2.62	158.66	H-Bond (Protein Donor)	false
O3P	O	HOH- 543	2.74	179.97	H-Bond (Protein Donor)	false
O3P	O	HOH- 546	2.7	179.97	H-Bond (Protein Donor)	false