scPDB - 1yim entry

Protein Data Bank Entry:

PDB ID : 1yim

Resolution :1.900 Å

Experimental Method : X-ray

Deposition Date : 2005-01-12

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Estrogen receptor
ID:	ESR1_HUMAN
AC:	P03372
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:	42.586
Number of residues:	39
Including
Standard Amino Acids:	38
Non Standard Amino Acids:	0
Water Molecules:	1
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.737	327.375

% Hydrophobic	% Polar
73.20	26.80
According to VolSite

Ligand :

HET Code:	CM4
Formula:	C28H32NO4
Molecular weight:	446.558 g/mol
DrugBank ID:	DB07567
Buried Surface Area:	74.2 %
Polar Surface area:	63.36 Å2

Number of
H-Bond Acceptors:	4
H-Bond Donors:	3
Rings:	5
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	6

Mass center Coordinates

X	Y	Z
31.536	-1.61555	25.4127

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
C21	SD	MET- 343	4.29	0	Hydrophobic	false
C4	CB	LEU- 346	4.36	0	Hydrophobic	false
C2	CB	LEU- 346	3.74	0	Hydrophobic	false
C22	CB	THR- 347	4.15	0	Hydrophobic	false
C27	CG2	THR- 347	3.65	0	Hydrophobic	false
C6	CD2	LEU- 349	3.83	0	Hydrophobic	false
C5	CB	ALA- 350	3.88	0	Hydrophobic	false
C24	CB	ALA- 350	3.53	0	Hydrophobic	false
N29	OD1	ASP- 351	2.59	161.12	H-Bond (Ligand Donor)	false
N29	OD1	ASP- 351	2.59	0	Ionic (Ligand Cationic)	false
O8	OE2	GLU- 353	2.67	146.73	H-Bond (Ligand Donor)	false
C32	CD2	LEU- 354	3.68	0	Hydrophobic	false
C32	CZ3	TRP- 383	3.83	0	Hydrophobic	false
C14	CD1	LEU- 384	4.21	0	Hydrophobic	false
C25	CD1	LEU- 384	4.33	0	Hydrophobic	false
C9	CB	LEU- 387	3.97	0	Hydrophobic	false
C24	CD1	LEU- 387	4.3	0	Hydrophobic	false
C12	CG	MET- 388	4.15	0	Hydrophobic	false
C14	CE	MET- 388	4.25	0	Hydrophobic	false
C9	CD2	LEU- 391	4.24	0	Hydrophobic	false
C12	CD2	LEU- 391	3.73	0	Hydrophobic	false
O8	NH2	ARG- 394	3.36	149.13	H-Bond (Protein Donor)	false
C12	CE1	PHE- 404	4.08	0	Hydrophobic	false
C19	SD	MET- 421	3.84	0	Hydrophobic	false
C16	CG1	ILE- 424	4.22	0	Hydrophobic	false
C12	CD1	LEU- 428	3.83	0	Hydrophobic	false
C16	CB	HIS- 524	4.47	0	Hydrophobic	false
O17	ND1	HIS- 524	2.61	154.39	H-Bond (Ligand Donor)	false
C14	CD2	LEU- 525	4.33	0	Hydrophobic	false
C15	CG	LEU- 525	3.67	0	Hydrophobic	false
C16	CD2	LEU- 525	3.82	0	Hydrophobic	false
C22	CD2	LEU- 525	4	0	Hydrophobic	false
C23	CD1	LEU- 525	3.68	0	Hydrophobic	false
C27	CB	CYS- 530	4.25	0	Hydrophobic	false
C31	CD1	LEU- 536	3.83	0	Hydrophobic	false