NPASS Compound

Structure

NPC225630 OpenBabel06302215342D 30 34 0 0 1 0 0 0 0 0999 V2000 2.2014 0.4506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2016 -0.2601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8171 -0.6152 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8172 -1.3258 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4327 -1.6810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2019 -1.6812 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5865 -1.3261 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5866 -2.1126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5863 -0.6155 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9709 -0.2602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9707 0.4506 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3554 -0.6154 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9710 -1.6815 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.3555 -1.3263 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2598 -1.6816 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8753 -1.3264 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5679 -1.6993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8754 -0.6155 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2602 -0.2602 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.2601 0.4504 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9413 0.8437 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3553 0.8059 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1022 -1.0468 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6620 -0.6156 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0548 -0.9159 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3617 1.5310 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2596 -2.4682 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3551 0.2468 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2021 -2.3919 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 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 6 1 0 0 0 0 6 7 1 0 0 0 0 6 30 1 1 0 0 0 7 13 1 0 0 0 0 7 8 1 1 0 0 0 7 9 1 0 0 0 0 9 10 1 1 0 0 0 11 10 1 6 0 0 0 11 12 1 0 0 0 0 11 22 1 0 0 0 0 12 26 1 0 0 0 0 12 13 1 0 0 0 0 12 18 1 0 0 0 0 13 14 1 0 0 0 0 14 15 1 0 0 0 0 14 29 1 0 0 0 0 15 16 1 0 0 0 0 15 28 1 0 0 0 0 16 17 1 0 0 0 0 16 18 1 0 0 0 0 16 25 1 0 0 0 0 18 19 1 0 0 0 0 18 24 1 0 0 0 0 19 20 1 0 0 0 0 19 23 1 6 0 0 0 20 21 2 0 0 0 0 20 22 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	622.26
Volume:	606.324
LogP:	2.942
LogD:	1.991
LogS:	-4.649
# Rotatable Bonds:	11
TPSA:	170.33
# H-Bond Aceptor:	13
# H-Bond Donor:	0
# Rings:	4
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.183
Synthetic Accessibility Score:	6.232
Fsp3:	0.742
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.147
MDCK Permeability:	0.00015498962602578104
Pgp-inhibitor:	1.0
Pgp-substrate:	0.042
Human Intestinal Absorption (HIA):	0.832
20% Bioavailability (F20%):	0.025
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.367
Plasma Protein Binding (PPB):	43.607276916503906%
Volume Distribution (VD):	1.565
Pgp-substrate:	32.553096771240234%

ADMET: Metabolism

CYP1A2-inhibitor:	0.008
CYP1A2-substrate:	0.01
CYP2C19-inhibitor:	0.011
CYP2C19-substrate:	0.076
CYP2C9-inhibitor:	0.001
CYP2C9-substrate:	0.006
CYP2D6-inhibitor:	0.408
CYP2D6-substrate:	0.048
CYP3A4-inhibitor:	0.359
CYP3A4-substrate:	0.396

ADMET: Excretion

Clearance (CL):	3.663
Half-life (T1/2):	0.75

ADMET: Toxicity

hERG Blockers:	0.021
Human Hepatotoxicity (H-HT):	0.95
Drug-inuced Liver Injury (DILI):	0.965
AMES Toxicity:	0.124
Rat Oral Acute Toxicity:	0.774
Maximum Recommended Daily Dose:	0.053
Skin Sensitization:	0.692
Carcinogencity:	0.179
Eye Corrosion:	0.799
Eye Irritation:	0.135
Respiratory Toxicity:	0.95

Download Data

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

Natural Product: NPC225630

Natural Product ID:	NPC225630
*Common Name:**	WYMLQUXVTATHIE-AGLSRPHKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	WYMLQUXVTATHIE-AGLSRPHKSA-N
Standard InCHI:	InChI=1S/C20H26O10/c1-6-4-8(21)12(23)17(2)7(6)5-9-19-11(17)10(22)13(24)18(3,30-16(19)27)20(19,28)14(25)15(26)29-9/h4,7,9-14,16,22-25,27-28H,5H2,1-3H3/t7-,9+,10+,11+,12+,13-,14-,16-,17-,18+,19+,20+/m0/s1
SMILES:	CC1=CC(=O)[C@H]([C@@]2(C)[C@H]1C[C@@H]1[C@@]34[C@@H]2[C@H]([C@@H]([C@](C)([C@@]4([C@H](C(=O)O1)O)O)O[C@@H]3O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11304852
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001283] Terpene lactones [CHEMONTID:0002119] Quassinoids

*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
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	seed	n.a.	DOI[10.1016/0031-9422(96)00258-0]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	fruit	n.a.	DOI[10.1016/S1383-5769(99)00023-9]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10086989]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1512598]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[15165151]
NPO15520	Dracocephalum kotschyi	Species	Lamiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[15949825]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	fruit	Indonesia	n.a.	PMID[17896817]
NPO15146	Myrica nana	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18723353]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	Vietnam	n.a.	PMID[19026551]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	seeds	n.a.	n.a.	PMID[20050684]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[22506620]
NPO15520	Dracocephalum kotschyi	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26522747]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6481366]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7561896]
NPO211	Aplysina cauliformis	Species	Aplysinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[8350091]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO15520	Dracocephalum kotschyi	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO15520	Dracocephalum kotschyi	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12089	Trifolium alexandrinum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO10818	Carpobrotus edulis	Species	Aizoaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14845	Ceratophyllum submersum	Species	Ceratophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14948	Brucea javanica	Species	Simaroubaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1641	Amycolatopsis azurea	Species	Pseudonocardiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO12089	Trifolium alexandrinum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11873	Oecophylla smaragdina	Species	Formicidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11432	Centrolobium tomentosum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12717	Parmelia metastrigosa	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9203	Cephalonomia gallicola	Species	Bethylidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO211	Aplysina cauliformis	Species	Aplysinidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26718	Chelidonura fulvipunctata	Species	Aglajidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15146	Myrica nana	Species	Myricaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11084	Asplenium normale	Species	Aspleniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14749	Lippia carviodora	Species	Verbenaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14150	Solanum jamaicense	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11637	Psilostrophe cooperi	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15520	Dracocephalum kotschyi	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12944	Sideritis tragoriganum	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5303	Castanea crenata	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3164	Yponomeuta malinellus	Species	Yponomeutidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14528	Pneumatospora obcoronata	n.a.	n.a.	n.a.	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 NPC225630 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	260
0.1-0.2	1587
0.2-0.3	4687
0.3-0.4	7798
0.4-0.5	11051
0.5-0.6	8202
0.6-0.7	5149
0.7-0.8	3098
0.8-0.85	684
0.85-0.9	134
0.9-0.95	34
0.95-1	13

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 NPC225630 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	228
0.1-0.2	1832
0.2-0.3	3884
0.3-0.4	2003
0.4-0.5	643
0.5-0.6	291
0.6-0.7	156
0.7-0.8	104
0.8-0.85	9
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