NPASS Compound

Natural Product: NPC99020

Natural Product ID	NPC99020
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	YJVMDLQSCPBESM-ZZAAMMQTSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	21578112
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

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 81 85 0 0 0 0 0 0 0 0999 V2000 5.8949 0.9302 -1.8933 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1010 1.0554 -0.5956 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2896 2.4417 -0.0693 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6420 -0.0092 0.3366 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9099 -1.3018 0.0402 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5193 -1.1808 0.6044 C 0 0 1 0 0 0 0 0 0 0 0 0 3.6234 -1.4262 2.1097 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1361 -2.6968 2.3587 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0348 0.2333 0.3860 C 0 0 1 0 0 0 0 0 0 0 0 0 3.6068 0.8399 -0.8694 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5281 0.3047 0.4158 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9528 1.1647 1.2414 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5093 1.3681 1.4024 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2206 0.6113 0.3036 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.6930 0.7584 0.4231 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0949 0.9386 1.8449 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1324 2.0574 -0.2813 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5965 2.2746 -0.1396 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4657 1.1412 -0.4965 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.9160 -0.2307 -0.2483 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5119 -0.8545 0.9900 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4159 -1.0950 -1.4272 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4296 -0.3028 -0.3286 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9019 -1.6655 0.0026 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4972 -1.7331 -0.5579 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6412 -0.7494 0.2136 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3330 -1.4269 1.5178 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7195 -0.5710 -0.4771 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5482 0.2220 -1.7665 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4160 -1.8482 -0.7833 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5736 -2.1707 0.0728 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7819 -3.3476 0.3766 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.6548 1.2503 0.2507 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8354 1.8454 -2.5044 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9472 0.7189 -1.5846 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5623 0.0781 -2.4907 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3137 2.9297 0.1893 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9525 2.4838 0.8264 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7645 3.1052 -0.8275 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7344 -0.1107 0.1414 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5047 0.3134 1.3751 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9364 -1.4597 -1.0421 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4530 -2.1095 0.6056 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5797 -1.3927 2.5091 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2154 -0.6612 2.6170 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5447 -3.2083 2.9430 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4342 0.8221 1.2344 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5659 0.1746 -1.7439 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0958 1.7871 -1.0593 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6273 1.7778 1.8572 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6873 2.4690 1.2549 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8694 1.0318 2.3959 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9318 1.1671 -0.6405 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1866 1.0518 1.9949 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7262 0.2019 2.5469 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6762 1.9377 2.1727 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8793 1.9808 -1.3624 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5790 2.8726 0.1856 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8456 3.1669 -0.7897 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7892 2.6631 0.9042 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8012 1.2819 -1.5652 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7745 -1.2490 1.7044 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2116 -0.1345 1.5094 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1856 -1.7325 0.7607 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7432 -0.9730 -2.2803 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4809 -2.1466 -1.0819 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4569 -0.7666 -1.6237 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1680 -0.1418 -1.4203 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9923 -1.9595 1.0434 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5217 -2.4135 -0.5700 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1641 -2.7684 -0.3309 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5234 -1.5010 -1.6178 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4763 -2.1768 1.3091 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1690 -2.0390 1.9051 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0342 -0.7936 2.3197 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3182 -0.1712 -2.4958 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4109 0.0637 -2.2627 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8243 1.2917 -1.6513 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7660 -2.7382 -0.8745 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8574 -1.7555 -1.8250 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8339 2.2055 0.3694 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 1 7 8 1 0 6 9 1 0 9 10 1 0 9 11 1 0 11 12 2 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 1 15 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 20 22 1 0 20 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 1 26 28 1 0 28 29 1 6 28 30 1 0 30 31 1 0 31 32 2 0 19 33 1 0 10 2 1 0 28 11 1 0 31 6 1 0 26 14 1 0 23 15 1 0 1 34 1 0 1 35 1 0 1 36 1 0 3 37 1 0 3 38 1 0 3 39 1 0 4 40 1 0 4 41 1 0 5 42 1 0 5 43 1 0 7 44 1 0 7 45 1 0 8 46 1 0 9 47 1 1 10 48 1 0 10 49 1 0 12 50 1 0 13 51 1 0 13 52 1 0 14 53 1 6 16 54 1 0 16 55 1 0 16 56 1 0 17 57 1 0 17 58 1 0 18 59 1 0 18 60 1 0 19 61 1 6 21 62 1 0 21 63 1 0 21 64 1 0 22 65 1 0 22 66 1 0 22 67 1 0 23 68 1 6 24 69 1 0 24 70 1 0 25 71 1 0 25 72 1 0 27 73 1 0 27 74 1 0 27 75 1 0 29 76 1 0 29 77 1 0 29 78 1 0 30 79 1 0 30 80 1 0 33 81 1 0 M END

Standard InCHIKey	YJVMDLQSCPBESM-ZZAAMMQTSA-N
Standard InCHI	InChI=1S/C30H48O3/c1-25(2)14-15-30(18-31)20(16-25)19-8-9-22-27(5)12-11-23(32)26(3,4)21(27)10-13-28(22,6)29(19,7)17-24(30)33/h8,20-23,31-32H,9-18H2,1-7H3/t20-,21-,22+,23-,27-,28+,29+,30+/m0/s1
SMILES	CC1(C)CC[C@@]2(CO)[C@@H](C1)C1=CC[C@@H]3[C@@]4(C)CC[C@@H](C(C)(C)[C@@H]4CC[C@@]3(C)[C@]1(C)CC2=O)O

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
NPO21437	Rhododendron aureum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20080	Lepisorus thunbergianus	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21437	Rhododendron aureum	Species	Ericaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20080	Lepisorus thunbergianus	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO20080	Lepisorus thunbergianus	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21437	Rhododendron aureum	Species	Ericaceae	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	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 NPC99020 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	19433
0.1-0.2	24923
0.2-0.3	4229
0.3-0.4	1005
0.4-0.5	189
0.5-0.6	60
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
0.7167	Intermediate Similarity	NPC101475
0.7049	Intermediate Similarity	NPC235341
0.7049	Intermediate Similarity	NPC253807
0.7049	Intermediate Similarity	NPC158662
0.6949	Remote Similarity	NPC290598
0.6949	Remote Similarity	NPC30590
0.6719	Remote Similarity	NPC246708
0.6613	Remote Similarity	NPC311078
0.6613	Remote Similarity	NPC34177
0.6418	Remote Similarity	NPC488519
0.6349	Remote Similarity	NPC196753
0.6269	Remote Similarity	NPC213412
0.6269	Remote Similarity	NPC2539
0.625	Remote Similarity	NPC480924
0.6154	Remote Similarity	NPC470588
0.6056	Remote Similarity	NPC294360
0.5938	Remote Similarity	NPC474989
0.5909	Remote Similarity	NPC159168
0.5854	Remote Similarity	NPC480937
0.5758	Remote Similarity	NPC475862
0.5714	Remote Similarity	NPC480934
0.5672	Remote Similarity	NPC238992
0.5672	Remote Similarity	NPC3915
0.5641	Remote Similarity	NPC167383
0.5571	Remote Similarity	NPC480946
0.5571	Remote Similarity	NPC130577
0.5571	Remote Similarity	NPC142415
0.5571	Remote Similarity	NPC102683
0.5556	Remote Similarity	NPC164349
0.5479	Remote Similarity	NPC480919
0.5441	Remote Similarity	NPC230295
0.5441	Remote Similarity	NPC53744
0.5441	Remote Similarity	NPC98386
0.5395	Remote Similarity	NPC283343
0.5385	Remote Similarity	NPC27765
0.5385	Remote Similarity	NPC122418
0.5385	Remote Similarity	NPC491014
0.5373	Remote Similarity	NPC237344
0.5362	Remote Similarity	NPC480950
0.5352	Remote Similarity	NPC198664
0.5342	Remote Similarity	NPC49776
0.5342	Remote Similarity	NPC63118
0.5342	Remote Similarity	NPC474436
0.5325	Remote Similarity	NPC473160
0.5303	Remote Similarity	NPC142754
0.5294	Remote Similarity	NPC40394
0.5278	Remote Similarity	NPC7260
0.5278	Remote Similarity	NPC182797
0.5278	Remote Similarity	NPC210037
0.5278	Remote Similarity	NPC120968
0.5278	Remote Similarity	NPC171203
0.5278	Remote Similarity	NPC307426
0.5278	Remote Similarity	NPC98442
0.5278	Remote Similarity	NPC242468
0.5278	Remote Similarity	NPC227467
0.5278	Remote Similarity	NPC273621
0.5278	Remote Similarity	NPC52169
0.5278	Remote Similarity	NPC488562
0.5256	Remote Similarity	NPC480920
0.5217	Remote Similarity	NPC95594
0.5195	Remote Similarity	NPC273668
0.5152	Remote Similarity	NPC120098
0.5139	Remote Similarity	NPC187722
0.5139	Remote Similarity	NPC191965
0.5139	Remote Similarity	NPC136313
0.5135	Remote Similarity	NPC228784
0.5135	Remote Similarity	NPC324341
0.5135	Remote Similarity	NPC601810
0.5122	Remote Similarity	NPC237503
0.5072	Remote Similarity	NPC478657
0.507	Remote Similarity	NPC40552
0.5068	Remote Similarity	NPC51700
0.5068	Remote Similarity	NPC88716
0.5068	Remote Similarity	NPC68160
0.5068	Remote Similarity	NPC112866
0.5063	Remote Similarity	NPC480921

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC99020 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6987
0.1-0.2	2090
0.2-0.3	69
0.3-0.4	3
0.4-0.5	0
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
0.5493	Remote Similarity	NPD7645	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