NPASS Compound

Structure

NPC57638 OpenBabel06302216112D 30 32 0 0 1 0 0 0 0 0999 V2000 0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 3.4641 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 0 0 0 2 3 1 0 0 0 0 3 4 1 0 0 0 0 3 5 1 0 0 0 0 3 6 1 0 0 0 0 6 26 2 0 0 0 0 6 7 1 0 0 0 0 7 8 2 0 0 0 0 7 30 1 0 0 0 0 8 9 1 0 0 0 0 8 15 1 0 0 0 0 9 10 1 0 0 0 0 10 11 1 0 0 0 0 10 14 1 6 0 0 0 11 12 2 0 0 0 0 11 13 1 0 0 0 0 15 16 2 0 0 0 0 15 29 1 0 0 0 0 16 26 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 28 1 0 0 0 0 23 24 1 0 0 0 0 23 27 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	412.15
Volume:	418.498
LogP:	4.123
LogD:	1.814
LogS:	-3.675
# Rotatable Bonds:	5
TPSA:	131.36
# H-Bond Aceptor:	7
# H-Bond Donor:	5
# Rings:	3
# Heavy Atoms:	7

MedChem Properties

QED Drug-Likeness Score:	0.245
Synthetic Accessibility Score:	3.915
Fsp3:	0.261
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.381
MDCK Permeability:	1.1554719094419852e-05
Pgp-inhibitor:	0.947
Pgp-substrate:	0.098
Human Intestinal Absorption (HIA):	0.307
20% Bioavailability (F20%):	0.441
30% Bioavailability (F30%):	0.018

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.005
Plasma Protein Binding (PPB):	93.67447662353516%
Volume Distribution (VD):	0.919
Pgp-substrate:	12.844067573547363%

ADMET: Metabolism

CYP1A2-inhibitor:	0.441
CYP1A2-substrate:	0.309
CYP2C19-inhibitor:	0.033
CYP2C19-substrate:	0.058
CYP2C9-inhibitor:	0.592
CYP2C9-substrate:	0.552
CYP2D6-inhibitor:	0.047
CYP2D6-substrate:	0.18
CYP3A4-inhibitor:	0.076
CYP3A4-substrate:	0.077

ADMET: Excretion

Clearance (CL):	1.095
Half-life (T1/2):	0.708

ADMET: Toxicity

hERG Blockers:	0.002
Human Hepatotoxicity (H-HT):	0.257
Drug-inuced Liver Injury (DILI):	0.972
AMES Toxicity:	0.662
Rat Oral Acute Toxicity:	0.686
Maximum Recommended Daily Dose:	0.941
Skin Sensitization:	0.918
Carcinogencity:	0.586
Eye Corrosion:	0.003
Eye Irritation:	0.882
Respiratory Toxicity:	0.336

Download Data

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

Natural Product: NPC57638

Natural Product ID:	NPC57638
*Common Name:**	WMHKGGITIQNIDV-CQSZACIVSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WMHKGGITIQNIDV-CQSZACIVSA-N
Standard InCHI:	InChI=1S/C23H24O7/c1-6-23(4,5)16-19(28)12(9-14(25)10(2)3)18(27)15-17(26)11-7-8-13(24)20(29)21(11)30-22(15)16/h6-8,14,24-25,27-29H,1-2,9H2,3-5H3/t14-/m1/s1
SMILES:	C=CC(C)(C)c1c(c(C[C@H](C(=C)C)O)c(c2c(=O)c3ccc(c(c3oc12)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones [CHEMONTID:0003517] 2-prenylated xanthones

*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
NPO19764	Tithonia diversifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11975495]
NPO24016	Cladanthus mixtus	Species	Asteraceae	Eukaryota	Roots	n.a.	n.a.	PMID[14738379]
NPO19764	Tithonia diversifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19299148]
NPO19764	Tithonia diversifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23501116]
NPO21003	Cystoseira tamariscifolia	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25640118]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19764	Tithonia diversifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO24016	Cladanthus mixtus	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16024	Piper sumatranum	Species	Piperaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13990	Montanoa atriplicifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19000	Crepis crocea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO825	Stranvaesia davidiana	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9019	Asplenium antiquum	Species	Aspleniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21675	Persicaria sibirica	Species	Polygonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21003	Cystoseira tamariscifolia	Species	Sargassaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3338	Vatica obscura	Species	Dipterocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27328	Echinopsis candicans	Species	Cactaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20927	Scirpophaga incertulas	Species	Crambidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15534	Parablechnum procerum	Species	Blechnaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19764	Tithonia diversifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO20116	Ilex cornuta	Species	Aquifoliaceae	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 NPC57638 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	439
0.1-0.2	1624
0.2-0.3	3739
0.3-0.4	9130
0.4-0.5	9241
0.5-0.6	3800
0.6-0.7	4927
0.7-0.8	5118
0.8-0.85	2446
0.85-0.9	1503
0.9-0.95	699
0.95-1	31

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 NPC57638 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	386
0.1-0.2	928
0.2-0.3	1793
0.3-0.4	2634
0.4-0.5	1857
0.5-0.6	944
0.6-0.7	424
0.7-0.8	126
0.8-0.85	34
0.85-0.9	15
0.9-0.95	9
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