scPDB - 4bl5 entry

Protein Data Bank Entry:

PDB ID : 4bl5

Resolution :2.600 Å

Experimental Method : X-ray

Deposition Date : 2013-05-01

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	GDP-L-fucose synthase
ID:	FCL_HUMAN
AC:	Q13630
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1.271

Chains:

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

Ligand binding site composition:

B-Factor:	34.903
Number of residues:	48
Including
Standard Amino Acids:	47
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NAP
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.548	482.625

% Hydrophobic	% Polar
46.15	53.85
According to VolSite

Ligand :

HET Code:	GFB
Formula:	C16H23N5O15P2
Molecular weight:	587.326 g/mol
DrugBank ID:	-
Buried Surface Area:	79.61 %
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
25.4009	8.94684	-87.0935

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
O3P	N	LEU- 76	2.66	176.47	H-Bond (Protein Donor)	false
C5'	CB	LEU- 76	3.75	0	Hydrophobic	false
C3'	CD2	LEU- 76	3.81	0	Hydrophobic	false
C2'	CE2	PHE- 77	4.02	0	Hydrophobic	false
O4	OG	SER- 114	3.44	124.87	H-Bond (Protein Donor)	false
O4	OG	SER- 114	3.44	129	H-Bond (Ligand Donor)	false
C1	SG	CYS- 116	3.72	0	Hydrophobic	false
C2A	CB	CYS- 116	4.45	0	Hydrophobic	false
C4A	SG	CYS- 116	3.23	0	Hydrophobic	false
C3	CE2	TYR- 143	4.4	0	Hydrophobic	false
C6A	CB	ASN- 172	4.44	0	Hydrophobic	false
O1X	ND2	ASN- 172	2.7	156.69	H-Bond (Protein Donor)	false
N2	O	GLY- 185	3.24	138.1	H-Bond (Ligand Donor)	false
O1P	ND1	HIS- 186	3.14	136.2	H-Bond (Protein Donor)	false
O1P	N	VAL- 187	2.96	140.09	H-Bond (Protein Donor)	false
C1'	CG2	VAL- 187	4.32	0	Hydrophobic	false
O6	NZ	LYS- 194	2.73	160.09	H-Bond (Protein Donor)	false
N7	N	TRP- 208	3.12	145.2	H-Bond (Protein Donor)	false
O1X	NE	ARG- 215	3.06	152.89	H-Bond (Protein Donor)	false
O2X	NH2	ARG- 215	3.09	178.39	H-Bond (Protein Donor)	false
O1X	CZ	ARG- 215	3.9	0	Ionic (Protein Cationic)	false
O2X	CZ	ARG- 215	3.94	0	Ionic (Protein Cationic)	false
C4'	CD1	ILE- 252	4.37	0	Hydrophobic	false
C1'	CG2	ILE- 252	4.16	0	Hydrophobic	false
O2'	O	SER- 276	2.89	171.59	H-Bond (Ligand Donor)	false
O5	NZ	LYS- 282	3.32	123.15	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 282	2.97	150.28	H-Bond (Protein Donor)	false
O1X	NZ	LYS- 282	2.97	0	Ionic (Protein Cationic)	false
C6A	C4N	NAP- 901	3.97	0	Hydrophobic	false