scPDB - 1nde entry

Protein Data Bank Entry:

PDB ID : 1nde

Resolution :3.000 Å

Experimental Method : X-ray

Deposition Date : 2002-12-09

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	7.820	7.820	7.820	0.000	7.820	1

List of CHEMBLId :

CHEMBL346455

Binding Site :

Uniprot Annotation

Name:	Estrogen receptor beta
ID:	ESR2_HUMAN
AC:	Q92731
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:	65.700
Number of residues:	41
Including
Standard Amino Acids:	41
Non Standard Amino Acids:	0
Water Molecules:	0
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.570	610.875

% Hydrophobic	% Polar
69.61	30.39
According to VolSite

Ligand :

HET Code:	MON
Formula:	C24H30ClN6OS
Molecular weight:	486.053 g/mol
DrugBank ID:	DB04020
Buried Surface Area:	73.05 %
Polar Surface area:	116.08 Å2

Number of
H-Bond Acceptors:	7
H-Bond Donors:	3
Rings:	4
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	1
Rule of Five Violation:	0
Rotatable Bonds:	10

Mass center Coordinates

X	Y	Z
108.808	7.81552	-107.134

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
S13	CG	MET- 295	4.46	0	Hydrophobic	false
C20	SD	MET- 295	4.23	0	Hydrophobic	false
C16	SD	MET- 295	3.58	0	Hydrophobic	false
C26	CD1	LEU- 298	4.24	0	Hydrophobic	false
C22	CD1	LEU- 301	4.03	0	Hydrophobic	false
C6	CB	ALA- 302	3.28	0	Hydrophobic	false
C15	CB	ALA- 302	3.26	0	Hydrophobic	false
C22	CB	ALA- 302	4.41	0	Hydrophobic	false
N14	OD1	ASP- 303	2.93	145.33	H-Bond (Ligand Donor)	false
N14	OD2	ASP- 303	3.27	131.79	H-Bond (Ligand Donor)	false
O31	OE2	GLU- 305	3.43	130.21	H-Bond (Ligand Donor)	false
C6	CZ3	TRP- 335	4.35	0	Hydrophobic	false
C30	CE	MET- 336	4.37	0	Hydrophobic	false
C25	CD2	LEU- 339	4.31	0	Hydrophobic	false
C24	CB	LEU- 339	3.61	0	Hydrophobic	false
C15	CD1	LEU- 339	3.55	0	Hydrophobic	false
CL33	CE	MET- 340	3.51	0	Hydrophobic	false
C30	CE	MET- 340	4.21	0	Hydrophobic	false
CL33	CD2	LEU- 343	4.39	0	Hydrophobic	false
C24	CB	LEU- 343	3.36	0	Hydrophobic	false
C17	CE2	PHE- 356	3.98	0	Hydrophobic	false
CL33	CZ	PHE- 356	3.96	0	Hydrophobic	false
C26	CD1	ILE- 373	3.43	0	Hydrophobic	false
C29	CG2	ILE- 373	4.27	0	Hydrophobic	false
C20	CG1	ILE- 373	3.67	0	Hydrophobic	false
CL33	CG2	ILE- 376	3.57	0	Hydrophobic	false
C27	CD1	ILE- 376	3.82	0	Hydrophobic	false
CL33	CD1	LEU- 380	3.27	0	Hydrophobic	false
C20	CB	HIS- 475	3.97	0	Hydrophobic	false
C5	CD1	LEU- 476	3.83	0	Hydrophobic	false
S13	CD1	LEU- 476	3.84	0	Hydrophobic	false
C16	CE	MET- 479	3.83	0	Hydrophobic	false