NPASS Compound

Natural Product: NPC335761

Natural Product ID	NPC335761
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Beta-Dihydrogedunol
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL464958
PubChem CID	40469671
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids [CHEMONTID:0002380] Limonoids

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 73 78 0 0 0 0 0 0 0 0999 V2000 -0.0131 4.1243 3.3322 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6864 3.4412 2.1954 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6571 3.9324 1.5953 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2238 2.2019 1.7737 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7958 1.4723 0.7027 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5217 0.3265 1.3351 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0502 -0.7140 0.4261 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4510 -1.1355 0.6178 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4652 -2.0426 1.8760 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3765 0.0101 1.0544 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0547 -1.9144 -0.4805 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.1687 -1.1750 -0.9694 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1803 -2.3897 -1.5744 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7698 -1.9221 -1.6296 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5863 -0.5292 -1.0180 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1200 -0.2459 -0.8643 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2045 1.1284 -0.3449 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0113 2.2000 -1.4355 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6446 1.2007 0.0352 C 0 0 1 0 0 0 0 0 0 0 0 0 2.4165 2.3237 -0.6222 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3062 2.1553 0.8087 C 0 0 2 0 0 0 0 0 0 0 0 0 3.5188 1.7134 1.5349 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7385 2.0690 2.7212 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4169 0.8886 0.8682 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9392 0.3251 -0.3283 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4506 -0.0528 -0.1781 C 0 0 2 0 0 0 0 0 0 0 0 0 2.1653 -0.8350 -1.4023 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7703 -0.6343 -1.9882 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3988 -0.8503 1.1183 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7637 -0.8341 -0.6879 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2458 -1.8921 0.0482 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9793 -2.7128 -0.7686 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9596 -2.1934 -1.9661 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2584 -1.0862 -1.9762 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3638 0.3714 -1.8671 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5096 5.0148 2.8814 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7299 4.4281 4.1217 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7322 3.4560 3.7850 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6282 2.1525 0.3297 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8584 -0.0510 2.1619 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4014 0.7559 1.8972 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4221 -1.6360 0.7006 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6840 -2.8039 1.8138 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4834 -2.4246 2.0172 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2040 -1.3628 2.7296 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1283 0.9658 0.6172 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4154 -0.2522 0.7009 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4478 0.1320 2.1329 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5849 -2.8385 -0.0810 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2727 -1.3367 -1.9265 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7055 -2.1337 -2.5461 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1243 -3.5220 -1.6383 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0817 -2.5936 -1.1091 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5042 -1.8034 -2.7225 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2215 -0.9460 -0.0359 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3838 1.9250 -2.4019 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0163 2.6370 -1.4012 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6444 3.0682 -1.1004 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9597 3.1410 1.1897 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9707 1.0881 -1.1599 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3412 -1.9217 -1.1421 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8466 -0.6438 -2.2549 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7611 -0.0083 -2.8758 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4758 -1.6646 -2.3504 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3078 -0.7044 1.7583 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3180 -1.9368 0.9485 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5839 -0.4618 1.8074 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0832 -2.0666 1.1191 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4701 -3.6290 -0.4154 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1293 -0.5123 -2.8824 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9168 1.1902 -1.4228 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6681 0.7359 -2.6852 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1426 -0.1613 -2.5024 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 8 10 1 0 8 11 1 0 11 12 1 0 11 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 6 17 19 1 0 19 20 1 6 20 21 1 0 21 22 1 0 22 23 2 0 22 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 26 29 1 1 25 30 1 0 30 31 1 0 31 32 2 0 32 33 1 0 33 34 1 0 15 35 1 6 17 5 1 0 21 19 1 0 34 30 2 0 15 7 1 0 28 16 1 0 26 19 1 0 1 36 1 0 1 37 1 0 1 38 1 0 5 39 1 6 6 40 1 0 6 41 1 0 7 42 1 1 9 43 1 0 9 44 1 0 9 45 1 0 10 46 1 0 10 47 1 0 10 48 1 0 11 49 1 1 12 50 1 0 13 51 1 0 13 52 1 0 14 53 1 0 14 54 1 0 16 55 1 1 18 56 1 0 18 57 1 0 18 58 1 0 21 59 1 1 25 60 1 6 27 61 1 0 27 62 1 0 28 63 1 0 28 64 1 0 29 65 1 0 29 66 1 0 29 67 1 0 31 68 1 0 32 69 1 0 34 70 1 0 35 71 1 0 35 72 1 0 35 73 1 0 M END

Standard InCHIKey	IVHWWYNBMIROCV-LMTLKJQUSA-N
Standard InCHI	InChI=1S/C28H38O7/c1-15(29)33-20-13-18-24(2,3)19(30)8-10-25(18,4)17-7-11-26(5)21(16-9-12-32-14-16)34-23(31)22-28(26,35-22)27(17,20)6/h9,12,14,17-22,30H,7-8,10-11,13H2,1-6H3/t17-,18+,19+,20-,21+,22-,25-,26+,27+,28-/m1/s1
SMILES	CC(=O)O[C@@H]1C[C@H]2C(C)(C)[C@@H](O)CC[C@@]2([C@@H]2[C@]1(C)[C@@]13O[C@@H]1C(=O)O[C@H]([C@@]3(CC2)C)c1ccoc1)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
NPO20413	Meliaceae spp.	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[9134742]
NPO20413	Meliaceae spp.	Species	Meliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20413	Meliaceae spp.	Species	Meliaceae	Eukaryota	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
IC50	4
Inhibition	2
Activity	3

Activity Type	# Activity
Cell line	1
Individual protein	4
Organism	4

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT72	Individual protein	Solute carrier organic anion transporter family member 1B3	Homo sapiens	IC50	=	3235.94	nM	PMID[23013356]
NPT72	Individual protein	Solute carrier organic anion transporter family member 1B3	Homo sapiens	Inhibition	=	23.84	%	PMID[24467317]
NPT73	Individual protein	Solute carrier organic anion transporter family member 1B1	Homo sapiens	Inhibition	=	20.54	%	PMID[23022281]
NPT73	Individual protein	Solute carrier organic anion transporter family member 1B1	Homo sapiens	IC50	=	1698.24	nM	PMID[26653328]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT91	Cell line	KB	Homo sapiens	Activity	=	69.0	%	PMID[22951040]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	4.21	ug.mL-1	PMID[21044847]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	IC50	=	2.44	ug.mL-1	PMID[19581457]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Activity	=	0.93	%	PMID[19618898]
NPT6	Organism	Plasmodium falciparum	Plasmodium falciparum	Activity	=	0.82	%	PMID[25089809]

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 NPC335761 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	11122
0.1-0.2	34609
0.2-0.3	3774
0.3-0.4	293
0.4-0.5	23
0.5-0.6	26
0.6-0.7	5
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
0.7808	Intermediate Similarity	NPC134254
0.7671	Intermediate Similarity	NPC107646
0.7467	Intermediate Similarity	NPC302369
0.7067	Intermediate Similarity	NPC602263
0.6883	Remote Similarity	NPC39986
0.6709	Remote Similarity	NPC209364
0.6709	Remote Similarity	NPC605015
0.6625	Remote Similarity	NPC475381
0.6341	Remote Similarity	NPC126723
0.5952	Remote Similarity	NPC472653
0.5854	Remote Similarity	NPC470939
0.5783	Remote Similarity	NPC5079
0.5765	Remote Similarity	NPC96443
0.5765	Remote Similarity	NPC290400
0.575	Remote Similarity	NPC604270
0.5747	Remote Similarity	NPC271235
0.5581	Remote Similarity	NPC237155
0.5529	Remote Similarity	NPC286722
0.5495	Remote Similarity	NPC472651
0.5455	Remote Similarity	NPC473753
0.5444	Remote Similarity	NPC302392
0.5426	Remote Similarity	NPC472652
0.5402	Remote Similarity	NPC473473
0.5402	Remote Similarity	NPC475295
0.5385	Remote Similarity	NPC469846
0.5287	Remote Similarity	NPC609366
0.5281	Remote Similarity	NPC117986
0.5238	Remote Similarity	NPC60973
0.5238	Remote Similarity	NPC605384
0.5227	Remote Similarity	NPC473766
0.5165	Remote Similarity	NPC25255
0.5114	Remote Similarity	NPC611370
0.5056	Remote Similarity	NPC305016
0.5055	Remote Similarity	NPC604177
0.5054	Remote Similarity	NPC123088

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC335761 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3698
0.1-0.2	5378
0.2-0.3	74
0.3-0.4	0
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