scPDB - 4yco entry

Protein Data Bank Entry:

PDB ID : 4yco

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2015-02-20

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	tRNA-dihydrouridine(16) synthase
ID:	DUSC_ECOLI
AC:	P33371
Organism:	Escherichia coli
Reign:	Bacteria
TaxID:	83333
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	39.195
Number of residues:	42
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.122	442.125

% Hydrophobic	% Polar
40.46	59.54
According to VolSite

Ligand :

HET Code:	FMN
Formula:	C17H19N4O9P
Molecular weight:	454.328 g/mol
DrugBank ID:	DB03247
Buried Surface Area:	68.83 %
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
1.47861	79.5515	275.051

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- 6	4.21	0	Hydrophobic	false
O2'	O	PRO- 7	2.88	172.69	H-Bond (Ligand Donor)	false
C6	CB	MET- 8	4.07	0	Hydrophobic	false
C9A	CG	MET- 8	4.25	0	Hydrophobic	false
C8	CE	MET- 8	3.89	0	Hydrophobic	false
N5	N	GLU- 9	2.96	164.49	H-Bond (Protein Donor)	false
C6	CB	GLU- 9	4.36	0	Hydrophobic	false
C7M	CG2	VAL- 11	3.93	0	Hydrophobic	false
O2	NE2	GLN- 68	2.84	160.27	H-Bond (Protein Donor)	false
N3	OE1	GLN- 68	2.95	165.37	H-Bond (Ligand Donor)	false
N1	NZ	LYS- 139	2.95	155.7	H-Bond (Protein Donor)	false
O2	NZ	LYS- 139	3.12	121.25	H-Bond (Protein Donor)	false
O3'	NZ	LYS- 139	2.89	146.31	H-Bond (Protein Donor)	false
C8M	CZ	TYR- 176	3.92	0	Hydrophobic	false
C4'	CE1	TYR- 176	3.76	0	Hydrophobic	false
O3'	OD1	ASN- 200	2.57	163.03	H-Bond (Ligand Donor)	false
O5'	ND2	ASN- 200	3.07	130.97	H-Bond (Protein Donor)	false
O1P	N	GLU- 202	2.83	173.38	H-Bond (Protein Donor)	false
O2P	N	GLY- 224	2.95	161.84	H-Bond (Protein Donor)	false
C8M	CG	ARG- 225	3.87	0	Hydrophobic	false
O1P	CZ	ARG- 225	3.68	0	Ionic (Protein Cationic)	false
O3P	CZ	ARG- 225	3.77	0	Ionic (Protein Cationic)	false
O1P	NH2	ARG- 225	2.83	176.8	H-Bond (Protein Donor)	false
O3P	N	ARG- 225	2.85	172.42	H-Bond (Protein Donor)	false
O3P	NE	ARG- 225	2.84	167.25	H-Bond (Protein Donor)	false
O2P	O	HOH- 526	2.7	179.95	H-Bond (Protein Donor)	false
O2P	O	HOH- 578	2.53	145.18	H-Bond (Protein Donor)	false