scPDB - 2ydf entry

Protein Data Bank Entry:

PDB ID : 2ydf

Resolution :2.750 Å

Experimental Method : X-ray

Deposition Date : 2011-03-18

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Serum albumin
ID:	ALBU_HUMAN
AC:	P02768
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	/

Chains:

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

Ligand binding site composition:

B-Factor:	17.931
Number of residues:	26
Including
Standard Amino Acids:	26
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.058	1485.000

% Hydrophobic	% Polar
54.32	45.68
According to VolSite

Ligand :

HET Code:	IO3
Formula:	C11H9I3O3
Molecular weight:	569.901 g/mol
DrugBank ID:	-
Buried Surface Area:	60.53 %
Polar Surface area:	63.19 Å2

Number of
H-Bond Acceptors:	3
H-Bond Donors:	0
Rings:	1
Aromatic rings:	1
Anionic atoms:	2
Cationic atoms:	0
Rule of Five Violation:	1
Rotatable Bonds:	4

Mass center Coordinates

X	Y	Z
4.74753	-10.9243	7.02294

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
I3	CE2	TYR- 150	3.66	0	Hydrophobic	false
O1	OH	TYR- 150	2.98	165.61	H-Bond (Protein Donor)	false
O2	NZ	LYS- 199	2.65	142.23	H-Bond (Protein Donor)	false
O2	NZ	LYS- 199	2.65	0	Ionic (Protein Cationic)	false
C11	CG	ARG- 218	4.33	0	Hydrophobic	false
I1	CD2	LEU- 219	3.74	0	Hydrophobic	false
C11	CD2	LEU- 219	3.36	0	Hydrophobic	false
O3	NH2	ARG- 222	2.83	121.57	H-Bond (Protein Donor)	false
I1	CZ	PHE- 223	4.2	0	Hydrophobic	false
C11	CD1	LEU- 238	3.65	0	Hydrophobic	false
C4	CD2	LEU- 238	3.95	0	Hydrophobic	false
I2	CG	ARG- 257	4.03	0	Hydrophobic	false
O1	NE	ARG- 257	2.84	135.45	H-Bond (Protein Donor)	false
O1	NH2	ARG- 257	2.98	129.1	H-Bond (Protein Donor)	false
I2	CD2	LEU- 260	3.85	0	Hydrophobic	false
I2	CB	ALA- 261	4.41	0	Hydrophobic	false
I1	CG2	ILE- 290	4.2	0	Hydrophobic	false
C3	CG2	ILE- 290	3.87	0	Hydrophobic	false
I3	CB	ALA- 291	3.93	0	Hydrophobic	false
C1	CB	ALA- 291	3.58	0	Hydrophobic	false
C6	CB	ALA- 291	3.39	0	Hydrophobic	false