scPDB - 1yet entry

Protein Data Bank Entry:

PDB ID : 1yet

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 1997-03-25

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	5.920	6.060	6.110	0.100	6.150	3

List of CHEMBLId :

CHEMBL278315

Binding Site :

Uniprot Annotation

Name:	Heat shock protein HSP 90-alpha
ID:	HS90A_HUMAN
AC:	P07900
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:	11.496
Number of residues:	35
Including
Standard Amino Acids:	32
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.739	546.750

% Hydrophobic	% Polar
41.98	58.02
According to VolSite

Ligand :

HET Code:	GDM
Formula:	C29H40N2O9
Molecular weight:	560.636 g/mol
DrugBank ID:	DB02424
Buried Surface Area:	58.28 %
Polar Surface area:	163.47 Å2

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

Mass center Coordinates

X	Y	Z
41.2017	-46.5482	65.6033

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
C25	CB	ASN- 51	3.86	0	Hydrophobic	false
C7	CB	ASN- 51	4.35	0	Hydrophobic	false
C26	CB	ALA- 55	3.99	0	Hydrophobic	false
O5	NZ	LYS- 58	2.82	155.59	H-Bond (Protein Donor)	false
C26	CD	LYS- 58	3.6	0	Hydrophobic	false
N2	OD2	ASP- 93	2.78	150.94	H-Bond (Ligand Donor)	false
C26	CG2	ILE- 96	3.69	0	Hydrophobic	false
C23	CE	MET- 98	3.65	0	Hydrophobic	false
C27	CG	MET- 98	4.09	0	Hydrophobic	false
C7	CE	MET- 98	3.99	0	Hydrophobic	false
C27	CB	ASP- 102	3.74	0	Hydrophobic	false
C27	CB	ASN- 106	4.15	0	Hydrophobic	false
C28	CB	ASN- 106	3.57	0	Hydrophobic	false
C22	CD1	LEU- 107	3.97	0	Hydrophobic	false
C23	CD2	LEU- 107	3.72	0	Hydrophobic	false
O9	NZ	LYS- 112	3.01	167	H-Bond (Protein Donor)	false
C22	CD	LYS- 112	4.37	0	Hydrophobic	false
O1	N	PHE- 138	2.76	161.24	H-Bond (Protein Donor)	false
C22	CB	PHE- 138	4.37	0	Hydrophobic	false
C23	CD1	PHE- 138	3.85	0	Hydrophobic	false
C23	CG1	VAL- 150	4.16	0	Hydrophobic	false
O4	O	HOH- 520	2.88	155.63	H-Bond (Protein Donor)	false