scPDB - 4ylf entry

Protein Data Bank Entry:

PDB ID : 4ylf

Resolution :2.300 Å

Experimental Method : X-ray

Deposition Date : 2015-03-05

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit homolog
ID:	PYRKH_THEMA
AC:	Q9X1X4
Organism:	Thermotoga maritima
Reign:	Bacteria
TaxID:	243274
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
C	95 %
D	5 %

Ligand binding site composition:

B-Factor:	66.416
Number of residues:	44
Including
Standard Amino Acids:	44
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.452	1407.375

% Hydrophobic	% Polar
48.20	51.80
According to VolSite

Ligand :

HET Code:	FAD
Formula:	C27H31N9O15P2
Molecular weight:	783.534 g/mol
DrugBank ID:	DB03147
Buried Surface Area:	64.68 %
Polar Surface area:	381.7 Å2

Number of
H-Bond Acceptors:	22
H-Bond Donors:	7
Rings:	6
Aromatic rings:	3
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
-29.3898	64.4916	45.5908

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
C7M	CG	PHE- 38	3.88	0	Hydrophobic	false
C4'	CD1	ILE- 50	4.11	0	Hydrophobic	false
O2'	O	PRO- 51	2.79	154.02	H-Bond (Ligand Donor)	false
C7	CB	PRO- 51	3.82	0	Hydrophobic	false
C8M	CG	PRO- 51	3.34	0	Hydrophobic	false
C8	CG	PRO- 51	3.39	0	Hydrophobic	false
C2'	CD2	LEU- 52	3.6	0	Hydrophobic	false
O4	N	THR- 53	2.93	156.95	H-Bond (Protein Donor)	false
O4	OG1	THR- 53	3.18	123.87	H-Bond (Protein Donor)	false
N5	OG1	THR- 53	2.91	157.73	H-Bond (Protein Donor)	false
N3	O	VAL- 67	2.51	150.19	H-Bond (Ligand Donor)	false
O2	N	LYS- 69	2.56	159.48	H-Bond (Protein Donor)	false
C3'	CG2	VAL- 71	4.35	0	Hydrophobic	false
C5'	CB	VAL- 71	4	0	Hydrophobic	false
C4B	CG1	VAL- 71	3.98	0	Hydrophobic	false
O1P	OG1	THR- 74	2.62	154.63	H-Bond (Protein Donor)	false
O1P	N	THR- 74	3.16	147.55	H-Bond (Protein Donor)	false
O2P	N	THR- 75	2.94	160.05	H-Bond (Protein Donor)	false
C4'	CG2	THR- 75	3.83	0	Hydrophobic	false
C8	CB	ASN- 215	4.15	0	Hydrophobic	false
N6A	O	MET- 218	3.19	153.01	H-Bond (Ligand Donor)	false
C7M	CE	MET- 218	3.79	0	Hydrophobic	false
C8M	SD	MET- 218	4.01	0	Hydrophobic	false
C7M	CG	PRO- 244	4.39	0	Hydrophobic	false
O1A	NE2	GLN- 266	2.54	155.53	H-Bond (Protein Donor)	false
O1P	NE2	GLN- 266	3.13	125.31	H-Bond (Protein Donor)	false