NPASS Compound

Natural Product: NPC102414

Natural Product ID	NPC102414
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	3-Epidehydrotrametenolic Acid
IUPAC Name	2-[(3S,5R,10S,13R,14R,17R)-3-hydroxy-4,4,10,13,14-pentamethyl-2,3,5,6,12,15,16,17-octahydro-1H-cyclopenta[a]phenanthren-17-yl]-6-methylhept-5-enoic acid
Synonyms	3-Epidehydrotrametenolic Acid
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL226995
PubChem CID	12133286
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 79 82 0 0 0 0 0 0 0 0999 V2000 5.7199 1.6259 3.1326 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8504 1.3529 1.6593 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9044 1.7520 0.8369 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0055 1.4954 -0.6115 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7214 0.7502 -1.0214 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5567 -0.5589 -0.3055 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2783 -1.2545 -0.7287 C 0 0 1 0 0 0 0 0 0 0 0 0 2.1186 -2.5595 0.0505 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6636 -2.5367 0.5620 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0288 -1.7699 -0.5415 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0129 -0.5727 -0.5668 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9391 0.1857 0.7180 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5109 0.3063 -1.6772 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7135 0.9847 -1.0989 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5539 0.1989 -0.4488 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3154 -1.2306 -0.2992 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3471 -2.0039 0.0503 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7267 -1.4763 0.3014 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8854 -0.1515 -0.4044 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7879 0.7349 0.1513 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6613 0.5314 1.6674 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0500 2.1815 -0.0510 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0135 2.4344 -1.2137 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3358 1.8606 -0.7358 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.2490 0.4014 -0.3800 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0454 -0.3299 -1.4779 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0281 0.1905 0.8898 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6799 2.6048 0.4135 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1400 -2.5930 -1.7818 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6781 -1.4732 -0.7313 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4785 -1.1044 -1.6040 O 0 0 0 0 0 0 0 0 0 0 0 0 4.8278 -2.7204 -0.1614 O 0 0 0 0 0 0 0 0 0 0 0 0 7.0521 0.6535 1.1385 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9066 2.6860 3.3765 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3639 0.9580 3.7317 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6596 1.4147 3.4455 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0439 2.2810 1.2787 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9152 1.0058 -0.9236 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8767 2.5118 -1.0999 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9304 1.4933 -0.6547 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6244 0.7138 -2.1049 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6691 -0.4021 0.7669 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4691 -1.5789 -1.8054 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8097 -2.6010 0.9288 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3142 -3.4474 -0.5697 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6017 -2.0975 1.5571 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3308 -3.5857 0.6351 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8391 0.0560 1.3493 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7500 1.2773 0.5248 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0956 -0.1396 1.3688 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1084 -0.2564 -2.5465 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1995 1.0293 -2.0487 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8176 2.0260 -1.2521 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1533 -3.0468 0.1489 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4186 -2.2076 -0.1877 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9770 -1.4592 1.3611 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6260 -0.3417 -1.4831 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2161 -0.4332 1.9336 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9832 1.3091 2.0979 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6092 0.6259 2.1868 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6446 2.5710 0.8388 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1704 2.8432 -0.0671 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6636 2.0142 -2.1528 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1414 3.5244 -1.2774 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0955 2.0880 -1.5121 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7548 -1.3763 -1.5533 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7266 0.1517 -2.4489 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1195 -0.1352 -1.3878 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1202 0.2464 0.6028 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9114 -0.8242 1.3213 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9056 1.0042 1.6323 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6553 2.5934 0.5287 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7125 -2.1817 -2.6042 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5169 -3.6327 -1.5819 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9050 -2.7559 -2.1664 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6713 -3.2667 -0.2626 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8120 -0.3560 0.7932 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8043 0.5748 1.9652 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4962 1.2166 0.3023 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 1 11 13 1 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 1 20 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 25 27 1 0 24 28 1 0 10 29 1 6 6 30 1 0 30 31 2 0 30 32 1 0 2 33 1 0 11 7 1 0 20 15 1 0 16 10 1 0 25 19 1 0 1 34 1 0 1 35 1 0 1 36 1 0 3 37 1 0 4 38 1 0 4 39 1 0 5 40 1 0 5 41 1 0 6 42 1 0 7 43 1 6 8 44 1 0 8 45 1 0 9 46 1 0 9 47 1 0 12 48 1 0 12 49 1 0 12 50 1 0 13 51 1 0 13 52 1 0 14 53 1 0 17 54 1 0 18 55 1 0 18 56 1 0 19 57 1 6 21 58 1 0 21 59 1 0 21 60 1 0 22 61 1 0 22 62 1 0 23 63 1 0 23 64 1 0 24 65 1 6 26 66 1 0 26 67 1 0 26 68 1 0 27 69 1 0 27 70 1 0 27 71 1 0 28 72 1 0 29 73 1 0 29 74 1 0 29 75 1 0 32 76 1 0 33 77 1 0 33 78 1 0 33 79 1 0 M END

Standard InCHIKey	QFPLAAZRZNKRRY-FHZHDSSISA-N
Standard InCHI	InChI=1S/C30H46O3/c1-19(2)9-8-10-20(26(32)33)21-13-17-30(7)23-11-12-24-27(3,4)25(31)15-16-28(24,5)22(23)14-18-29(21,30)6/h9,11,14,20-21,24-25,31H,8,10,12-13,15-18H2,1-7H3,(H,32,33)/t20?,21-,24+,25+,28-,29-,30+/m1/s1
SMILES	CC(=CCCC([C@H]1CC[C@@]2([C@]1(C)CC=C1C2=CC[C@@H]2[C@]1(C)CC[C@@H](C2(C)C)O)C)C(=O)O)C

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
NPO33546	Poria coco	Species	n.a.	Eukaryota	n.a.	Yunnan, Kunming, China	n.a.	PMID[17488130]
NPO10608	Exodermis poria	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[COCONUT]
NPO10608	Exodermis poria	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[HerDing]
NPO10608	Exodermis poria	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[TCMID]

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

Activity Type	# Activity
Inhibition	4
Activity	1

Activity Type	# Activity
Cell line	1
Organism	4

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
NPT80	Cell line	Raji	Homo sapiens	Activity	=	70.0	%	PMID[17488130]
NPT164	Organism	Human herpesvirus 4	Human herpesvirus 4	Inhibition	=	9.2	%	PMID[17488130]
NPT164	Organism	Human herpesvirus 4	Human herpesvirus 4	Inhibition	=	45.3	%	PMID[17488130]
NPT164	Organism	Human herpesvirus 4	Human herpesvirus 4	Inhibition	=	79.1	%	PMID[17488130]
NPT164	Organism	Human herpesvirus 4	Human herpesvirus 4	Inhibition	=	100.0	%	PMID[17488130]

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 NPC102414 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	20774
0.1-0.2	24835
0.2-0.3	3770
0.3-0.4	363
0.4-0.5	65
0.5-0.6	30
0.6-0.7	15
0.7-0.8	0
0.8-0.85	1
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC84271
0.8833	High Similarity	NPC469406
0.8065	Intermediate Similarity	NPC77168
0.746	Intermediate Similarity	NPC222845
0.746	Intermediate Similarity	NPC296577
0.6866	Remote Similarity	NPC608955
0.6769	Remote Similarity	NPC83569
0.6769	Remote Similarity	NPC233836
0.6769	Remote Similarity	NPC159046
0.6769	Remote Similarity	NPC187376
0.6618	Remote Similarity	NPC48647
0.6613	Remote Similarity	NPC205455
0.6567	Remote Similarity	NPC212948
0.6377	Remote Similarity	NPC482518
0.6324	Remote Similarity	NPC142361
0.6324	Remote Similarity	NPC474684
0.6119	Remote Similarity	NPC196827
0.6	Remote Similarity	NPC45324
0.6	Remote Similarity	NPC162001
0.6	Remote Similarity	NPC203035
0.5915	Remote Similarity	NPC484975
0.5915	Remote Similarity	NPC186810
0.5915	Remote Similarity	NPC214697
0.5915	Remote Similarity	NPC321301
0.5882	Remote Similarity	NPC475772
0.5821	Remote Similarity	NPC202389
0.5758	Remote Similarity	NPC6707
0.5753	Remote Similarity	NPC141401
0.5714	Remote Similarity	NPC173272
0.5556	Remote Similarity	NPC138536
0.5522	Remote Similarity	NPC147568
0.5493	Remote Similarity	NPC76895
0.5479	Remote Similarity	NPC475921
0.5479	Remote Similarity	NPC474704
0.5479	Remote Similarity	NPC477812
0.5455	Remote Similarity	NPC72507
0.5417	Remote Similarity	NPC69279
0.5405	Remote Similarity	NPC484968
0.5362	Remote Similarity	NPC231310
0.5342	Remote Similarity	NPC66429
0.5263	Remote Similarity	NPC484797
0.5224	Remote Similarity	NPC20853
0.5211	Remote Similarity	NPC55309
0.5211	Remote Similarity	NPC28252
0.5195	Remote Similarity	NPC39082
0.5195	Remote Similarity	NPC610107
0.5139	Remote Similarity	NPC469400
0.5135	Remote Similarity	NPC470375
0.5135	Remote Similarity	NPC470376
0.5135	Remote Similarity	NPC310470

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC102414 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6517
0.1-0.2	2559
0.2-0.3	72
0.3-0.4	2
0.4-0.5	0
0.5-0.6	0
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
		NPD

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