scPDB - 3zy5 entry

Protein Data Bank Entry:

PDB ID : 3zy5

Resolution :1.960 Å

Experimental Method : X-ray

Deposition Date : 2011-08-17

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	GDP-fucose protein O-fucosyltransferase 1
ID:	OFUT1_CAEEL
AC:	Q18014
Organism:	Caenorhabditis elegans
Reign:	Eukaryota
TaxID:	6239
EC Number:	2.4.1.221

Chains:

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

Ligand binding site composition:

B-Factor:	22.196
Number of residues:	37
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.145	634.500

% Hydrophobic	% Polar
43.09	56.91
According to VolSite

Ligand :

HET Code:	GFB
Formula:	C16H23N5O15P2
Molecular weight:	587.326 g/mol
DrugBank ID:	-
Buried Surface Area:	66.04 %
Polar Surface area:	332.47 Å2

Number of
H-Bond Acceptors:	18
H-Bond Donors:	7
Rings:	4
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	8

Mass center Coordinates

X	Y	Z
-11.3461	-28.8209	18.0228

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
C3'	CB	ARG- 40	4.18	0	Hydrophobic	false
C4'	CD	ARG- 40	3.85	0	Hydrophobic	false
O3'	N	PHE- 41	3.26	133.09	H-Bond (Protein Donor)	false
O1P	N	GLY- 42	2.77	146.88	H-Bond (Protein Donor)	false
O3P	N	ASN- 43	3.11	157.95	H-Bond (Protein Donor)	false
O3	ND2	ASN- 43	3.11	156.19	H-Bond (Protein Donor)	false
N7	NE2	HIS- 238	3.07	155.51	H-Bond (Protein Donor)	false
C5'	CD	ARG- 240	4.48	0	Hydrophobic	false
O1	NH2	ARG- 240	2.98	174.37	H-Bond (Protein Donor)	false
O5	NH2	ARG- 240	3.22	120.16	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 240	3.41	124.54	H-Bond (Protein Donor)	false
O2X	NE	ARG- 240	2.56	171.86	H-Bond (Protein Donor)	false
O2X	CZ	ARG- 240	3.4	0	Ionic (Protein Cationic)	false
C1	CZ3	TRP- 245	4.15	0	Hydrophobic	false
C6A	CE3	TRP- 245	4.5	0	Hydrophobic	false
C6A	CG1	VAL- 248	4.1	0	Hydrophobic	false
C3	CE1	PHE- 261	4.3	0	Hydrophobic	false
C4A	CZ	PHE- 261	4.03	0	Hydrophobic	false
C5A	CE2	PHE- 261	3.72	0	Hydrophobic	false
C1'	CB	ASP- 309	4.19	0	Hydrophobic	false
N2	O	ASP- 334	2.92	123.35	H-Bond (Ligand Donor)	false
C2'	CE	MET- 336	3.67	0	Hydrophobic	false
O2X	OG	SER- 355	2.68	164.14	H-Bond (Protein Donor)	false
O1X	OG1	THR- 356	2.7	169.52	H-Bond (Protein Donor)	false
O1X	N	THR- 356	2.58	156.09	H-Bond (Protein Donor)	false
C3'	CD1	PHE- 357	3.89	0	Hydrophobic	false
C2'	CE1	PHE- 357	4.41	0	Hydrophobic	false