scPDB - 1i5r entry

Protein Data Bank Entry:

PDB ID : 1i5r

Resolution :1.600 Å

Experimental Method : X-ray

Deposition Date : 2001-02-28

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:	8.520	8.520	8.520	0.000	8.520	1

List of CHEMBLId :

CHEMBL371948

Binding Site :

Uniprot Annotation

Name:	Estradiol 17-beta-dehydrogenase 1
ID:	DHB1_HUMAN
AC:	P14061
Organism:	Homo sapiens
Reign:	Eukaryota
TaxID:	9606
EC Number:	1.1.1.62

Chains:

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

Ligand binding site composition:

B-Factor:	18.460
Number of residues:	64
Including
Standard Amino Acids:	61
Non Standard Amino Acids:	0
Water Molecules:	3
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
1.350	1086.750

% Hydrophobic	% Polar
58.07	41.93
According to VolSite

Ligand :

HET Code:	HYC
Formula:	C37H51N5O7
Molecular weight:	677.830 g/mol
DrugBank ID:	DB02323
Buried Surface Area:	70.67 %
Polar Surface area:	186.06 Å2

Number of
H-Bond Acceptors:	11
H-Bond Donors:	5
Rings:	7
Aromatic rings:	3
Anionic atoms:	0
Cationic atoms:	0
Rule of Five Violation:	3
Rotatable Bonds:	13

Mass center Coordinates

X	Y	Z
12.9193	0.763959	-6.56167

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
O33	OG	SER- 11	2.74	151.72	H-Bond (Ligand Donor)	false
O33	N	SER- 11	3.42	123.84	H-Bond (Protein Donor)	false
O33	OG	SER- 12	3.39	140.25	H-Bond (Protein Donor)	false
N46	OD1	ASP- 65	2.73	150.29	H-Bond (Ligand Donor)	false
N41	N	VAL- 66	2.92	159.36	H-Bond (Protein Donor)	false
O34	N	GLY- 92	2.85	161.93	H-Bond (Protein Donor)	false
C12	CB	VAL- 143	3.77	0	Hydrophobic	false
C2	CE	MET- 147	3.64	0	Hydrophobic	false
C18	CD1	LEU- 149	3.54	0	Hydrophobic	false
C3	CD2	LEU- 149	3.95	0	Hydrophobic	false
C5	CD1	LEU- 149	3.9	0	Hydrophobic	false
C8	CD1	LEU- 149	3.58	0	Hydrophobic	false
O17	OH	TYR- 155	2.94	138.51	H-Bond (Protein Donor)	false
C18	CE2	TYR- 155	3.68	0	Hydrophobic	false
C21	CZ	TYR- 155	3.64	0	Hydrophobic	false
C23	CE1	TYR- 155	4.01	0	Hydrophobic	false
C28	CE1	PHE- 192	3.93	0	Hydrophobic	false
C35	CE1	PHE- 192	4.07	0	Hydrophobic	false
C26	CZ	PHE- 192	3.44	0	Hydrophobic	false
C32	CE	MET- 193	3.87	0	Hydrophobic	false
C25	CG	GLU- 194	3.78	0	Hydrophobic	false
C6	CZ	TYR- 218	3.92	0	Hydrophobic	false
O3	NE2	HIS- 221	2.53	133.77	H-Bond (Ligand Donor)	false
C6	CB	SER- 222	4.01	0	Hydrophobic	false
C7	CG1	VAL- 225	4.4	0	Hydrophobic	false
C9	CG1	VAL- 225	4.15	0	Hydrophobic	false
C4	CG2	VAL- 225	3.71	0	Hydrophobic	false
C5	CG1	VAL- 225	3.87	0	Hydrophobic	false
C10	CG1	VAL- 225	3.76	0	Hydrophobic	false
C7	CE1	PHE- 226	3.68	0	Hydrophobic	false
C16	CZ	PHE- 226	3.98	0	Hydrophobic	false
C15	CE1	PHE- 226	3.96	0	Hydrophobic	false
C1	CE1	PHE- 259	3.11	0	Hydrophobic	false
C11	CZ	PHE- 259	4.38	0	Hydrophobic	false
C2	CD1	LEU- 262	4.39	0	Hydrophobic	false
C3	SD	MET- 279	4.15	0	Hydrophobic	false
O32	O	HOH- 404	3.22	179.97	H-Bond (Protein Donor)	false