scPDB - 1ry8 entry

Protein Data Bank Entry:

PDB ID : 1ry8

Resolution :1.690 Å

Experimental Method : X-ray

Deposition Date : 2003-12-19

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Aldo-keto reductase family 1 member C3
ID:	AK1C3_HUMAN
AC:	P42330
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	19.983
Number of residues:	41
Including
Standard Amino Acids:	40
Non Standard Amino Acids:	1
Water Molecules:	0
Cofactors:	NDP
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.033	1053.000

% Hydrophobic	% Polar
57.05	42.95
According to VolSite

Ligand :

HET Code:	RUT
Formula:	C27H29O16
Molecular weight:	609.510 g/mol
DrugBank ID:	DB01698
Buried Surface Area:	62.79 %
Polar Surface area:	268.34 Å2

Number of
H-Bond Acceptors:	16
H-Bond Donors:	9
Rings:	5
Aromatic rings:	2
Anionic atoms:	1
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
12.2461	-15.8942	48.4305

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
C7	CE2	TYR- 24	3.37	0	Hydrophobic	false
C12	CB	TYR- 24	4.31	0	Hydrophobic	false
C5	CB	PRO- 26	4.1	0	Hydrophobic	false
C15	CD2	LEU- 54	3.49	0	Hydrophobic	false
C14	CD2	LEU- 54	3.42	0	Hydrophobic	false
O6	OH	TYR- 55	2.86	140.44	H-Bond (Ligand Donor)	false
O7	OH	TYR- 55	2.68	163.8	H-Bond (Protein Donor)	false
C12	CE2	TYR- 55	3.38	0	Hydrophobic	false
C21	CH2	TRP- 86	4.34	0	Hydrophobic	false
O7	NE2	HIS- 117	2.69	142.81	H-Bond (Ligand Donor)	false
C27	CE	MET- 120	3.41	0	Hydrophobic	false
O9	OG	SER- 129	3.08	146.66	H-Bond (Protein Donor)	false
O14	OH	TYR- 216	2.93	163.75	H-Bond (Ligand Donor)	false
C5	CB	ASP- 224	3.24	0	Hydrophobic	false
O3	NE1	TRP- 227	3.09	122.35	H-Bond (Protein Donor)	false
O4	NE1	TRP- 227	3.09	137.86	H-Bond (Protein Donor)	false
C18	CH2	TRP- 227	3.98	0	Hydrophobic	false
C17	CZ2	TRP- 227	4.35	0	Hydrophobic	false
C16	CZ	PHE- 306	4.2	0	Hydrophobic	false
C26	CE1	PHE- 306	3.96	0	Hydrophobic	false
C20	CZ	PHE- 306	3.63	0	Hydrophobic	false
C24	CD1	PHE- 306	3.59	0	Hydrophobic	false
C27	CB	SER- 308	3.71	0	Hydrophobic	false
C27	CD1	PHE- 311	4.2	0	Hydrophobic	false
C25	CZ	TYR- 319	4.4	0	Hydrophobic	false
C27	CE2	TYR- 319	4.01	0	Hydrophobic	false
O15	OH	TYR- 319	2.76	145.78	H-Bond (Ligand Donor)	false
O6	N1N	NDP- 3324	3.38	121.03	H-Bond (Ligand Donor)	false
O13	O7N	NDP- 3324	2.71	163.76	H-Bond (Ligand Donor)	false
C23	C4N	NDP- 3324	4.41	0	Hydrophobic	false