scPDB - 2y4s entry

Protein Data Bank Entry:

PDB ID : 2y4s

Resolution :2.100 Å

Experimental Method : X-ray

Deposition Date : 2011-01-10

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Limit dextrinase
ID:	Q9S7S8_HORVU
AC:	Q9S7S8
Organism:	Hordeum vulgare
Reign:	Eukaryota
TaxID:	4513
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	16.284
Number of residues:	32
Including
Standard Amino Acids:	28
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.040	357.750

% Hydrophobic	% Polar
48.11	51.89
According to VolSite

Ligand :

HET Code:	BCD
Formula:	C42H70O35
Molecular weight:	1134.984 g/mol
DrugBank ID:	DB03995
Buried Surface Area:	32.95 %
Polar Surface area:	554.05 Å2

Number of
H-Bond Acceptors:	35
H-Bond Donors:	21
Rings:	9
Aromatic rings:	0
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	7

Mass center Coordinates

X	Y	Z
49.7017	36.995	33.0362

Binding mode :

What is Poseview ?

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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
C66	CD2	LEU- 474	4.48	0	Hydrophobic	false
C25	CE3	TRP- 512	4.08	0	Hydrophobic	false
C65	CB	TRP- 512	4.12	0	Hydrophobic	false
C16	CE2	TRP- 512	3.93	0	Hydrophobic	false
C45	CD2	TRP- 512	3.92	0	Hydrophobic	false
C65	CD1	PHE- 514	3.86	0	Hydrophobic	false
C25	CB	ASP- 541	4.44	0	Hydrophobic	false
O25	OD2	ASP- 541	2.78	177.65	H-Bond (Ligand Donor)	false
O25	NH2	ARG- 544	3.01	153.96	H-Bond (Protein Donor)	false
O35	NH1	ARG- 544	2.97	154.74	H-Bond (Protein Donor)	false
O35	NH2	ARG- 544	3.46	133.11	H-Bond (Protein Donor)	false
C34	CB	ASN- 551	4.45	0	Hydrophobic	false
C35	CG	PRO- 552	4.48	0	Hydrophobic	false
O22	O	PHE- 553	3.29	157.37	H-Bond (Ligand Donor)	false
O32	O	PHE- 553	2.67	129.63	H-Bond (Ligand Donor)	false
C33	CB	PHE- 553	4.19	0	Hydrophobic	false
C34	CD2	PHE- 553	4.48	0	Hydrophobic	false
C31	CD1	PHE- 553	3.94	0	Hydrophobic	false
C32	CB	PHE- 553	3.81	0	Hydrophobic	false
C55	CE2	PHE- 553	3.87	0	Hydrophobic	false
C36	CZ	PHE- 553	3.83	0	Hydrophobic	false
C57	CE1	PHE- 553	3.82	0	Hydrophobic	false
O36	OD1	ASN- 643	3.2	143.95	H-Bond (Ligand Donor)	false
O27	O	HOH- 2558	2.76	179.95	H-Bond (Protein Donor)	false