NPASS Compound

Structure

NPC86675 OpenBabel06302215242D 41 47 0 0 1 0 0 0 0 0999 V2000 5.0904 1.0426 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9732 1.5521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8558 1.0424 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8557 0.0232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9729 -0.4864 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0903 0.0234 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2075 -0.4861 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2074 -1.4576 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.3660 -1.9433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5247 -1.4574 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6828 -1.9434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8415 -1.4577 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8413 -0.4857 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6832 0.0003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5248 -0.4859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3662 -0.0003 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8418 1.4579 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8416 2.4299 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7129 2.9329 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0003 2.9156 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0003 3.8877 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8415 4.3738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6834 3.8878 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6834 2.9157 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8416 2.4296 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8417 1.4581 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0001 0.9719 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8419 0.4860 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7403 -0.4806 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5267 -1.0518 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4146 -0.6565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5161 0.3102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7298 0.8814 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2009 -1.2277 0.0000 O 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 -2.5661 4.3975 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8831 4.3973 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7078 1.9579 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6828 -2.9434 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0900 -1.9674 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7385 1.5519 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 3 41 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 7 6 1 1 0 0 0 7 8 1 0 0 0 0 7 16 1 0 0 0 0 8 9 1 0 0 0 0 8 40 1 6 0 0 0 9 10 1 0 0 0 0 10 15 2 0 0 0 0 10 11 1 0 0 0 0 11 12 2 0 0 0 0 11 39 1 0 0 0 0 12 13 1 0 0 0 0 13 35 1 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 14 17 1 0 0 0 0 15 16 1 0 0 0 0 17 27 1 0 0 0 0 17 18 1 0 0 0 0 17 38 1 6 0 0 0 18 19 2 0 0 0 0 18 20 1 0 0 0 0 20 25 2 0 0 0 0 20 21 1 0 0 0 0 21 22 2 0 0 0 0 21 37 1 0 0 0 0 22 23 1 0 0 0 0 23 24 2 0 0 0 0 23 36 1 0 0 0 0 24 25 1 0 0 0 0 25 26 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 1 0 0 0 27 35 1 0 0 0 0 28 33 2 0 0 0 0 28 29 1 0 0 0 0 29 30 2 0 0 0 0 30 31 1 0 0 0 0 31 32 2 0 0 0 0 31 34 1 0 0 0 0 32 33 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	558.12
Volume:	529.959
LogP:	3.696
LogD:	2.667
LogS:	-3.933
# Rotatable Bonds:	2
TPSA:	186.37
# H-Bond Aceptor:	11
# H-Bond Donor:	7
# Rings:	7
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.192
Synthetic Accessibility Score:	4.579
Fsp3:	0.167
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.401
MDCK Permeability:	5.469978532346431e-06
Pgp-inhibitor:	0.033
Pgp-substrate:	0.02
Human Intestinal Absorption (HIA):	0.614
20% Bioavailability (F20%):	0.978
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.003
Plasma Protein Binding (PPB):	95.01847076416016%
Volume Distribution (VD):	0.526
Pgp-substrate:	2.2821242809295654%

ADMET: Metabolism

CYP1A2-inhibitor:	0.185
CYP1A2-substrate:	0.088
CYP2C19-inhibitor:	0.156
CYP2C19-substrate:	0.059
CYP2C9-inhibitor:	0.727
CYP2C9-substrate:	0.895
CYP2D6-inhibitor:	0.056
CYP2D6-substrate:	0.182
CYP3A4-inhibitor:	0.77
CYP3A4-substrate:	0.691

ADMET: Excretion

Clearance (CL):	2.823
Half-life (T1/2):	0.666

ADMET: Toxicity

hERG Blockers:	0.083
Human Hepatotoxicity (H-HT):	0.135
Drug-inuced Liver Injury (DILI):	0.966
AMES Toxicity:	0.782
Rat Oral Acute Toxicity:	0.377
Maximum Recommended Daily Dose:	0.049
Skin Sensitization:	0.884
Carcinogencity:	0.899
Eye Corrosion:	0.003
Eye Irritation:	0.856
Respiratory Toxicity:	0.025

Download Data

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

Natural Product: NPC86675

Natural Product ID:	NPC86675
*Common Name:**	SJKVDYNUXFTAEE-SAOSBABKSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SJKVDYNUXFTAEE-SAOSBABKSA-N
Standard InCHI:	InChI=1S/C30H22O11/c31-15-5-1-13(2-6-15)26-21(36)11-18-19(34)12-23-25(27(18)39-26)29(38)28(37)24-20(35)9-17(33)10-22(24)40-30(29,41-23)14-3-7-16(32)8-4-14/h1-10,12,21,26,31-36,38H,11H2/t21-,26+,29+,30+/m1/s1
SMILES:	c1cc(ccc1[C@H]1[C@@H](Cc2c(cc3c(c2O1)[C@@]1(C(=O)c2c(cc(cc2O[C@@]1(c1ccc(cc1)O)O3)O)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	15984106
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001586] Biflavonoids and polyflavonoids

*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
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	flower	n.a.	PMID[21916433]
NPO19803	Oxytropis ochrocephala	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22494026]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	flower buds	n.a.	n.a.	PMID[23558238]
NPO14508	Aconitum heterophyllum	Species	Ranunculaceae	Eukaryota	n.a.	root	n.a.	PMID[24156713]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27228307]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	Roots	n.a.	n.a.	PMID[31150241]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31860304]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32223193]
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32997496]
NPO19303	Auricularia auricula-judae	Species	Auriculariaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO14508	Aconitum heterophyllum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO12444	Astragalus sinicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO19303	Auricularia auricula-judae	Species	Auriculariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18816	Lindera glauca	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18816	Lindera glauca	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18393	Eugenia sandwicensis	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO12444	Astragalus sinicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16416	Serratula strangulata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO19303	Auricularia auricula-judae	Species	Auriculariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO14508	Aconitum heterophyllum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO12444	Astragalus sinicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO19303	Auricularia auricula-judae	Species	Auriculariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19479	Trametes feei	Species	Coriolaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15287	Vernonia megapotamica	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13505	Grateloupia livida	Species	Halymeniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10882	Acer caudatifolium	Species	Aceraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14015	Salacia cordata	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12444	Astragalus sinicus	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10705	Marshallia graminifolia	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17558	Cynoglossum formosanum	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12376	Baccharis macraei	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7037	Rumohra adiantiformis	Species	Dryopteridaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18393	Eugenia sandwicensis	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17135	Mikania goyazensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19803	Oxytropis ochrocephala	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9756	Daphne genkwa	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18816	Lindera glauca	Species	Lauraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14508	Aconitum heterophyllum	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO19406	Chrysanthemum leptophyllum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4035	Daphne odora	Species	Thymelaeaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16416	Serratula strangulata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18247	Globicephala melas	Species	Delphinidae	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 NPC86675 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	432
0.1-0.2	1744
0.2-0.3	3741
0.3-0.4	9070
0.4-0.5	9177
0.5-0.6	4291
0.6-0.7	5597
0.7-0.8	5329
0.8-0.85	2571
0.85-0.9	715
0.9-0.95	27
0.95-1	3

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 NPC86675 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	394
0.1-0.2	912
0.2-0.3	1815
0.3-0.4	2676
0.4-0.5	1874
0.5-0.6	971
0.6-0.7	321
0.7-0.8	139
0.8-0.85	39
0.85-0.9	9
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