NPASS Compound

Structure

NPC251767 OpenBabel06302215212D 24 26 0 0 1 0 0 0 0 0999 V2000 5.0134 1.9284 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1781 2.4109 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1783 3.3756 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3425 1.9288 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5070 2.4115 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6712 1.9292 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6709 0.9643 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5065 0.4816 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3423 0.9638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1776 0.4813 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8353 0.4821 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6707 -0.0007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.9648 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0001 1.9294 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8357 2.4116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8358 3.3763 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8352 1.4473 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6706 1.9299 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8356 0.4826 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6712 0.0004 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6710 0.9651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0002 -0.9645 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7538 -1.5659 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 9 2 0 0 0 0 4 5 1 0 0 0 0 5 6 2 0 0 0 0 6 15 1 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 11 1 0 0 0 0 8 9 1 0 0 0 0 9 10 1 0 0 0 0 11 22 1 0 0 0 0 11 12 1 1 0 0 0 11 13 1 0 0 0 0 14 13 1 6 0 0 0 14 15 1 0 0 0 0 14 17 1 0 0 0 0 15 16 2 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 19 21 1 0 0 0 0 19 22 1 0 0 0 0 22 23 1 6 0 0 0 23 24 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	328.17
Volume:	348.149
LogP:	3.122
LogD:	1.908
LogS:	-4.064
# Rotatable Bonds:	2
TPSA:	71.44
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.667
Synthetic Accessibility Score:	4.937
Fsp3:	0.55
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.777
MDCK Permeability:	2.4413309802184813e-05
Pgp-inhibitor:	0.047
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.02
20% Bioavailability (F20%):	0.375
30% Bioavailability (F30%):	0.506

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.156
Plasma Protein Binding (PPB):	72.59192657470703%
Volume Distribution (VD):	1.392
Pgp-substrate:	11.156501770019531%

ADMET: Metabolism

CYP1A2-inhibitor:	0.236
CYP1A2-substrate:	0.793
CYP2C19-inhibitor:	0.247
CYP2C19-substrate:	0.75
CYP2C9-inhibitor:	0.257
CYP2C9-substrate:	0.678
CYP2D6-inhibitor:	0.402
CYP2D6-substrate:	0.173
CYP3A4-inhibitor:	0.746
CYP3A4-substrate:	0.49

ADMET: Excretion

Clearance (CL):	7.949
Half-life (T1/2):	0.132

ADMET: Toxicity

hERG Blockers:	0.011
Human Hepatotoxicity (H-HT):	0.132
Drug-inuced Liver Injury (DILI):	0.669
AMES Toxicity:	0.016
Rat Oral Acute Toxicity:	0.579
Maximum Recommended Daily Dose:	0.882
Skin Sensitization:	0.266
Carcinogencity:	0.738
Eye Corrosion:	0.005
Eye Irritation:	0.552
Respiratory Toxicity:	0.723

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC251767

Natural Product ID:	NPC251767
*Common Name:**	DLYLYXIDKXMSDL-GQWAEJPESA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	DLYLYXIDKXMSDL-GQWAEJPESA-N
Standard InCHI:	InChI=1S/C20H24O4/c1-10(2)11-6-12-14(7-15(11)22)20(5)8-13(17(12)23)18(24)19(3,4)16(20)9-21/h6-7,9-10,13,16,22H,8H2,1-5H3/t13-,16+,20+/m0/s1
SMILES:	CC(C)c1cc2c(cc1O)[C@@]1(C)C[C@@H](C2=O)C(=O)C(C)(C)[C@H]1C=O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000048] Tetralins

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO17318	Streptomyces cyaneus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[21462031]
NPO15612	Glaucium oxylobum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15612	Glaucium oxylobum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15612	Glaucium oxylobum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5124	Aconitum ibukiense	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12311	Graphis handelii	Species	Graphidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14653	Haliotis diversicolor	Species	Haliotidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14339	Fevillea trilobata	Species	Cucurbitaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25141	Mycetinis alliaceus	Species	Omphalotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15612	Glaucium oxylobum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17251	Aniba firmula	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3705	Anacardium humile	Species	Anacardiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13361	Clerodendrum tomentosum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17158	Trichocereus bridgesii	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17318	Streptomyces cyaneus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]

☑ Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

☑ Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC251767 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	309
0.1-0.2	1492
0.2-0.3	2938
0.3-0.4	7799
0.4-0.5	11019
0.5-0.6	6733
0.6-0.7	9181
0.7-0.8	2865
0.8-0.85	294
0.85-0.9	46
0.9-0.95	19
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID

Chemically structural similarity: II. Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC251767 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	281
0.1-0.2	971
0.2-0.3	1350
0.3-0.4	2603
0.4-0.5	2257
0.5-0.6	1200
0.6-0.7	427
0.7-0.8	57
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

Bioactivity similarity: Similar Natural Products in NPASS

Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.

Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data