scPDB - 2y5k entry

Protein Data Bank Entry:

PDB ID : 2y5k

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2011-01-14

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Fructose-1,6-bisphosphatase 1
ID:	F16P1_HUMAN
AC:	P09467
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	3.1.3.11

Chains:

Chain Name:	Percentage of Residues within binding site
B	78 %
D	22 %

Ligand binding site composition:

B-Factor:	27.672
Number of residues:	39
Including
Standard Amino Acids:	36
Non Standard Amino Acids:	1
Water Molecules:	2
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.374	702.000

% Hydrophobic	% Polar
51.92	48.08
According to VolSite

Ligand :

HET Code:	YCU
Formula:	C17H23N5O6S2
Molecular weight:	457.524 g/mol
DrugBank ID:	-
Buried Surface Area:	58.23 %
Polar Surface area:	184.36 Å2

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

Mass center Coordinates

X	Y	Z
30.8648	2.42183	36.8336

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
C25	CG1	VAL- 17	3.62	0	Hydrophobic	false
C29	SD	MET- 18	3.96	0	Hydrophobic	false
C23	CB	GLU- 20	4.15	0	Hydrophobic	false
C25	CB	GLU- 20	3.56	0	Hydrophobic	false
C16	CG	ARG- 22	3.22	0	Hydrophobic	false
S4	CB	ALA- 24	3.79	0	Hydrophobic	false
C23	CB	ALA- 24	4.34	0	Hydrophobic	false
N11	O	GLY- 26	2.75	161.14	H-Bond (Ligand Donor)	false
N22	O	GLY- 26	3.36	134.08	H-Bond (Ligand Donor)	false
S4	CD2	LEU- 30	4.07	0	Hydrophobic	false
C25	CD2	LEU- 30	4.36	0	Hydrophobic	false
C27	CD2	LEU- 30	4.28	0	Hydrophobic	false
O18	N	THR- 31	2.89	164.31	H-Bond (Protein Donor)	false
O20	OG1	THR- 31	2.69	173.99	H-Bond (Protein Donor)	false
C29	CG2	THR- 31	3.73	0	Hydrophobic	false
C23	SD	MET- 177	4.3	0	Hydrophobic	false
C25	CE	MET- 177	3.99	0	Hydrophobic	false
C30	CB	MET- 177	4.06	0	Hydrophobic	false
C30	CB	ASP- 178	4.39	0	Hydrophobic	false
O21	O	HOH- 2242	2.83	179.96	H-Bond (Protein Donor)	false