scPDB - 3uyl entry

Protein Data Bank Entry:

PDB ID : 3uyl

Resolution :1.850 Å

Experimental Method : X-ray

Deposition Date : 2011-12-06

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Probable NDP-rhamnosyltransferase
ID:	Q9ALM8_9PSEU
AC:	Q9ALM8
Organism:	Saccharopolyspora spinosa
Reign:	Bacteria
TaxID:	60894
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	18.820
Number of residues:	38
Including
Standard Amino Acids:	37
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.343	1171.125

% Hydrophobic	% Polar
47.26	52.74
According to VolSite

Ligand :

HET Code:	TYD
Formula:	C10H13N2O11P2
Molecular weight:	399.165 g/mol
DrugBank ID:	DB03103
Buried Surface Area:	69.39 %
Polar Surface area:	220.27 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	2
Rings:	2
Aromatic rings:	0
Anionic atoms:	3
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
13.1008	49.9972	-18.8348

Binding mode :

What is Poseview ?

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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
O2A	OG1	THR- 12	2.94	141.89	H-Bond (Protein Donor)	false
O3A	OG1	THR- 12	3.29	143.95	H-Bond (Protein Donor)	false
C4'	CE	MET- 15	4.22	0	Hydrophobic	false
O3'	ND2	ASN- 202	3.1	152.43	H-Bond (Protein Donor)	false
C1'	CB	ASN- 202	3.99	0	Hydrophobic	false
C5M	SG	CYS- 223	4.48	0	Hydrophobic	false
C5M	CB	PRO- 257	4.43	0	Hydrophobic	false
N3	O	VAL- 277	2.72	167.74	H-Bond (Ligand Donor)	false
O4	N	VAL- 277	3.29	128.79	H-Bond (Protein Donor)	false
C2'	CD2	LEU- 279	3.72	0	Hydrophobic	false
O2	N	LEU- 279	2.84	145.64	H-Bond (Protein Donor)	false
O2A	N	GLY- 296	2.65	149.78	H-Bond (Protein Donor)	false
O1A	OG1	THR- 297	2.85	164.69	H-Bond (Protein Donor)	false
O1A	N	THR- 297	3.15	155.81	H-Bond (Protein Donor)	false