scPDB - 4b8z entry

Protein Data Bank Entry:

PDB ID : 4b8z

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2012-08-31

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
D	100 %

Ligand binding site composition:

B-Factor:	82.538
Number of residues:	49
Including
Standard Amino Acids:	48
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	GDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.155	810.000

% Hydrophobic	% Polar
47.08	52.92
According to VolSite

Ligand :

HET Code:	NAP
Formula:	C21H25N7O17P3
Molecular weight:	740.381 g/mol
DrugBank ID:	DB03461
Buried Surface Area:	67.53 %
Polar Surface area:	405.54 Å2

Number of
H-Bond Acceptors:	21
H-Bond Donors:	5
Rings:	5
Aromatic rings:	3
Anionic atoms:	4
Cationic atoms:	1
Rule of Five Violation:	2
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
13.614	35.2873	-65.3192

Binding mode :

What is Poseview ?

2D View
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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
O3B	OG	SER- 16	2.63	160.24	H-Bond (Ligand Donor)	false
O3B	N	SER- 16	3.21	127.61	H-Bond (Protein Donor)	false
O1A	N	LEU- 18	2.79	158.42	H-Bond (Protein Donor)	false
O2N	N	VAL- 19	2.87	173.15	H-Bond (Protein Donor)	false
C5D	CG2	VAL- 19	3.96	0	Hydrophobic	false
O2X	OG	SER- 43	2.73	159.14	H-Bond (Protein Donor)	false
O2X	N	SER- 43	3.16	164	H-Bond (Protein Donor)	false
N6A	OD1	ASP- 47	3.07	141.01	H-Bond (Ligand Donor)	false
N1A	N	LEU- 48	3.02	170.37	H-Bond (Protein Donor)	false
O3D	O	LEU- 69	2.95	142.15	H-Bond (Ligand Donor)	false
C5D	CB	LEU- 69	3.82	0	Hydrophobic	false
C1B	CB	ALA- 70	4.38	0	Hydrophobic	false
C3D	CB	ALA- 71	4.07	0	Hydrophobic	false
C2D	CG2	VAL- 73	3.73	0	Hydrophobic	false
C4D	SG	CYS- 112	3.94	0	Hydrophobic	false
C3D	CB	CYS- 112	4.36	0	Hydrophobic	false
C5N	CB	SER- 114	3.75	0	Hydrophobic	false
O2D	OH	TYR- 143	2.61	162.82	H-Bond (Ligand Donor)	false
O2D	NZ	LYS- 147	2.84	156.63	H-Bond (Protein Donor)	false
C5N	CB	PRO- 170	4.12	0	Hydrophobic	false
O7N	N	VAL- 173	2.81	166.76	H-Bond (Protein Donor)	false
C4N	CG2	VAL- 173	3.67	0	Hydrophobic	false
O1A	CZ	ARG- 320	3.51	0	Ionic (Protein Cationic)	false
O1A	NH1	ARG- 320	2.86	149.08	H-Bond (Protein Donor)	false
O1A	NH2	ARG- 320	3.31	131.38	H-Bond (Protein Donor)	false
O2A	NH2	ARG- 320	2.99	146.59	H-Bond (Protein Donor)	false