NPASS Compound

Structure

NPC56021 OpenBabel06302215292D 23 26 0 0 1 0 0 0 0 0999 V2000 4.8960 -3.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3960 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8960 -3.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2620 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.2620 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3960 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.5299 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.5299 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5299 -2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6639 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7979 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7979 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9319 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9319 -0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0624 0.9914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7979 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6639 0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6639 -1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.5299 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9659 -0.2588 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2588 -0.9659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.3960 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 9 1 0 0 0 0 2 3 1 0 0 0 0 2 4 1 0 0 0 0 4 5 1 0 0 0 0 5 6 1 0 0 0 0 6 7 1 0 0 0 0 6 23 1 6 0 0 0 7 18 1 0 0 0 0 7 8 1 6 0 0 0 7 9 1 0 0 0 0 9 10 1 1 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 14 15 1 1 0 0 0 14 16 1 0 0 0 0 14 20 1 0 0 0 0 16 17 1 0 0 0 0 17 18 1 0 0 0 0 17 19 1 1 0 0 0 18 12 1 1 0 0 0 20 21 1 6 0 0 0 20 22 1 0 0 0 0 21 22 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	314.08
Volume:	308.569
LogP:	3.16
LogD:	2.756
LogS:	-3.792
# Rotatable Bonds:	3
TPSA:	89.13
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.772
Synthetic Accessibility Score:	2.304
Fsp3:	0.118
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.818
MDCK Permeability:	1.4996983736637048e-05
Pgp-inhibitor:	0.009
Pgp-substrate:	0.956
Human Intestinal Absorption (HIA):	0.032
20% Bioavailability (F20%):	0.053
30% Bioavailability (F30%):	0.986

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.014
Plasma Protein Binding (PPB):	92.13018035888672%
Volume Distribution (VD):	0.821
Pgp-substrate:	10.731465339660645%

ADMET: Metabolism

CYP1A2-inhibitor:	0.97
CYP1A2-substrate:	0.947
CYP2C19-inhibitor:	0.732
CYP2C19-substrate:	0.068
CYP2C9-inhibitor:	0.685
CYP2C9-substrate:	0.929
CYP2D6-inhibitor:	0.657
CYP2D6-substrate:	0.921
CYP3A4-inhibitor:	0.807
CYP3A4-substrate:	0.208

ADMET: Excretion

Clearance (CL):	7.5
Half-life (T1/2):	0.844

ADMET: Toxicity

hERG Blockers:	0.04
Human Hepatotoxicity (H-HT):	0.075
Drug-inuced Liver Injury (DILI):	0.812
AMES Toxicity:	0.457
Rat Oral Acute Toxicity:	0.041
Maximum Recommended Daily Dose:	0.774
Skin Sensitization:	0.727
Carcinogencity:	0.071
Eye Corrosion:	0.006
Eye Irritation:	0.918
Respiratory Toxicity:	0.523

Download Data

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

Natural Product: NPC56021

Natural Product ID:	NPC56021
*Common Name:**	PIJPBDSFAHXVGP-HXBCMNQYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	PIJPBDSFAHXVGP-HXBCMNQYSA-N
Standard InCHI:	InChI=1S/C20H32O3/c1-18(2)8-7-15(22)20(4)14(18)6-5-12-9-19(3,16-11-23-16)10-13(21)17(12)20/h9,13-17,21-22H,5-8,10-11H2,1-4H3/t13-,14-,15-,16+,17+,19+,20-/m1/s1
SMILES:	CC1(C)CC[C@H]([C@@]2(C)[C@@H]1CCC1=C[C@@](C)(C[C@H]([C@@H]21)O)[C@@H]1CO1)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids

*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
NPO25572	Symplocos lancifolia	Species	Symplocaceae	Eukaryota	n.a.	leaf	n.a.	PMID[21288041]
NPO25572	Symplocos lancifolia	Species	Symplocaceae	Eukaryota	leaves	Bac Quang, Ha Giang Province, in Vietnam	n.a.	PMID[21288041]
NPO24415	Dioscorea alata	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO24415	Dioscorea alata	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO24415	Dioscorea alata	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO25572	Symplocos lancifolia	Species	Symplocaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13307	Agave gracilipes	Species	Asparagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26521	Haematomma ventosum	Species	Haematommataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24824	Spongia cerebriformis	Species	Spongiidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25764	Dendrobium wardianum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24415	Dioscorea alata	Species	Dioscoreaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26043	Malbranchea cinnamomea	Species	n.a.	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26702	Vellozia epidendroides	Species	Velloziaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25182	Vernonia hirsuta	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO23681	Brickellia kellermanii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26104	Cinchona pubescens	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25990	Aeollanthus parvifolius	Species	Lamiaceae	Eukaryota	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 NPC56021 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	201
0.1-0.2	1579
0.2-0.3	5632
0.3-0.4	15335
0.4-0.5	9048
0.5-0.6	5697
0.6-0.7	4209
0.7-0.8	903
0.8-0.85	61
0.85-0.9	31
0.9-0.95	1
0.95-1	0

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 NPC56021 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	183
0.1-0.2	1884
0.2-0.3	4061
0.3-0.4	2162
0.4-0.5	494
0.5-0.6	203
0.6-0.7	135
0.7-0.8	28
0.8-0.85	0
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