NPASS Compound

Natural Product: NPC137252

Natural Product ID	NPC137252
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	OLMIQOIPLQDJFU-KGLIPLIRSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	102322865
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001969] Dibenzylbutane lignans

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 48 50 0 0 0 0 0 0 0 0999 V2000 1.1731 -1.5847 -1.3357 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4828 -0.4245 -0.6211 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9939 -0.3350 0.7978 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4772 -0.1166 0.7586 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9088 1.1865 0.7092 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2899 1.3756 0.6766 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1595 0.3089 0.6935 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6939 -0.9866 0.7434 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3333 -1.1944 0.7762 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5863 -2.0691 0.7603 O 0 0 0 0 0 0 0 0 0 0 0 0 6.5270 0.5035 0.6609 O 0 0 0 0 0 0 0 0 0 0 0 0 7.1506 1.7539 0.6094 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0061 -0.6191 -0.5980 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.3358 -1.9139 0.1558 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6703 0.5579 0.0140 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1574 0.4240 0.0455 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8576 -0.1254 1.0693 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2369 -0.2177 1.0275 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8984 0.2639 -0.0860 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2240 0.8289 -1.1466 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8415 0.8965 -1.0528 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1448 1.2237 -2.1236 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.3912 1.3418 -1.4624 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2514 0.3315 -0.4561 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2456 -1.2936 -1.4444 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7688 -1.7459 -2.3327 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1492 -2.4725 -0.6833 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6933 0.5176 -1.1648 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5215 0.5299 1.2959 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8076 -1.2813 1.3442 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2105 1.9999 0.6970 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6439 2.3889 0.6378 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9828 -2.2154 0.8174 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8862 -2.4609 1.6444 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0501 2.2498 1.6157 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2340 1.5842 0.4020 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7067 2.4489 -0.1318 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3310 -0.7410 -1.6689 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4330 -2.1420 -0.0040 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1532 -1.7842 1.2347 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7959 -2.7811 -0.2341 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4344 1.4658 -0.5620 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3708 0.7137 1.0708 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3094 -0.4922 1.9248 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8123 -0.6466 1.8217 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3241 1.3434 -1.8945 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5062 2.3398 -1.0166 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1907 1.0653 -2.1628 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 2 0 5 6 1 0 6 7 2 0 7 8 1 0 8 9 2 0 8 10 1 0 7 11 1 0 11 12 1 0 2 13 1 0 13 14 1 0 13 15 1 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 2 0 20 22 1 0 22 23 1 0 23 24 1 0 9 4 1 0 21 16 1 0 24 19 1 0 1 25 1 0 1 26 1 0 1 27 1 0 2 28 1 6 3 29 1 0 3 30 1 0 5 31 1 0 6 32 1 0 9 33 1 0 10 34 1 0 12 35 1 0 12 36 1 0 12 37 1 0 13 38 1 6 14 39 1 0 14 40 1 0 14 41 1 0 15 42 1 0 15 43 1 0 17 44 1 0 18 45 1 0 21 46 1 0 23 47 1 0 23 48 1 0 M END

Standard InCHIKey	OLMIQOIPLQDJFU-KGLIPLIRSA-N
Standard InCHI	InChI=1S/C20H24O4/c1-13(8-15-4-6-18(22-3)17(21)10-15)14(2)9-16-5-7-19-20(11-16)24-12-23-19/h4-7,10-11,13-14,21H,8-9,12H2,1-3H3/t13-,14+/m1/s1
SMILES	C[C@H](Cc1ccc(c(c1)O)OC)[C@@H](C)Cc1ccc2c(c1)OCO2

Calculated Properties

Physi-Chem Properties

MedChem Properties

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

ADMET: Distribution

ADMET: Metabolism

ADMET: Excretion

ADMET: Toxicity

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO7850	Schisandra propinqua	Species	Schisandraceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1002/cjoc.20010190319]
NPO7850	Schisandra propinqua	Species	Schisandraceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1016/j.tet.2008.10.079]
NPO7850	Schisandra propinqua	Species	Schisandraceae	Eukaryota	n.a.	stem	n.a.	PMID[11395273]
NPO7850	Schisandra propinqua	Species	Schisandraceae	Eukaryota	n.a.	stem	n.a.	PMID[18536373]
NPO7850	Schisandra propinqua	Species	Schisandraceae	Eukaryota	aerial parts	Erlang Mountain area of Sichuan Province, China	2007-SEP	PMID[19413342]
NPO7850	Schisandra propinqua	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20681569]
NPO7850	Schisandra propinqua	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7374	Seseli montanum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO7850	Schisandra propinqua	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO7374	Seseli montanum	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7850	Schisandra propinqua	Species	Schisandraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11167	Prunus ssiori	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9834	Veronica austriaca	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6903	Lecanora straminea	Species	Lecanoraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7128	Cynthia savignyi	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	Organism Name	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

Molecular-level activity

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

In vitro activity

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

In vivo activity

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

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

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 toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC137252 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	22107
0.1-0.2	22341
0.2-0.3	4664
0.3-0.4	587
0.4-0.5	103
0.5-0.6	37
0.6-0.7	12
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.7708	Intermediate Similarity	NPC274356
0.7708	Intermediate Similarity	NPC101748
0.7273	Intermediate Similarity	NPC344161
0.7143	Intermediate Similarity	NPC80241
0.7143	Intermediate Similarity	NPC301641
0.7143	Intermediate Similarity	NPC485483
0.6875	Remote Similarity	NPC249788
0.66	Remote Similarity	NPC485480
0.6545	Remote Similarity	NPC487677
0.6545	Remote Similarity	NPC487675
0.6545	Remote Similarity	NPC46880
0.64	Remote Similarity	NPC232275
0.6316	Remote Similarity	NPC106739
0.6207	Remote Similarity	NPC471505
0.6102	Remote Similarity	NPC487679
0.6102	Remote Similarity	NPC487678
0.6	Remote Similarity	NPC227217
0.6	Remote Similarity	NPC117780
0.5882	Remote Similarity	NPC485482
0.5862	Remote Similarity	NPC487681
0.5818	Remote Similarity	NPC28398
0.5763	Remote Similarity	NPC161249
0.5714	Remote Similarity	NPC284464
0.5682	Remote Similarity	NPC165106
0.566	Remote Similarity	NPC104077
0.566	Remote Similarity	NPC219671
0.566	Remote Similarity	NPC147616
0.5625	Remote Similarity	NPC470626
0.5625	Remote Similarity	NPC40352
0.5625	Remote Similarity	NPC213711
0.5577	Remote Similarity	NPC196937
0.5536	Remote Similarity	NPC135777
0.5532	Remote Similarity	NPC76451
0.537	Remote Similarity	NPC63574
0.5306	Remote Similarity	NPC298757
0.5238	Remote Similarity	NPC282291
0.5238	Remote Similarity	NPC166137
0.5238	Remote Similarity	NPC169973
0.5217	Remote Similarity	NPC31279
0.5208	Remote Similarity	NPC165133
0.5208	Remote Similarity	NPC242885
0.5208	Remote Similarity	NPC95614
0.5208	Remote Similarity	NPC232316
0.5208	Remote Similarity	NPC477886
0.5192	Remote Similarity	NPC56214
0.5192	Remote Similarity	NPC476748
0.5179	Remote Similarity	NPC143895
0.5161	Remote Similarity	NPC145569
0.5102	Remote Similarity	NPC604144
0.5098	Remote Similarity	NPC600801
0.5091	Remote Similarity	NPC30951
0.5091	Remote Similarity	NPC192255
0.5091	Remote Similarity	NPC474288
0.5088	Remote Similarity	NPC165128
0.5085	Remote Similarity	NPC6369

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC137252 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3851
0.1-0.2	4990
0.2-0.3	291
0.3-0.4	13
0.4-0.5	3
0.5-0.6	1
0.6-0.7	0
0.7-0.8	0
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
0.5682	Remote Similarity	NPD5283	Phase 2

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by 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