NPASS Compound

Natural Product: NPC144660

Natural Product ID	NPC144660
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Methyl Ganoderate B
IUPAC Name	methyl (6R)-6-[(3S,5R,7S,10S,13R,14R,17R)-3,7-dihydroxy-4,4,10,13,14-pentamethyl-11,15-dioxo-2,3,5,6,7,12,16,17-octahydro-1H-cyclopenta[a]phenanthren-17-yl]-2-methyl-4-oxoheptanoate
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1087181
PubChem CID	21632955
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 84 87 0 0 0 0 0 0 0 0999 V2000 3.9203 -2.2880 0.1401 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0261 -1.0646 0.4032 C 0 0 2 0 0 0 0 0 0 0 0 0 3.5614 -0.3784 1.5792 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9492 0.1344 1.4817 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5339 0.4721 2.5320 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7306 0.2953 0.2498 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1156 0.8483 0.4966 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0746 2.2065 1.1542 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8815 1.0046 -0.7603 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9587 0.3901 -0.9417 O 0 0 0 0 0 0 0 0 0 0 0 0 7.4291 1.8363 -1.7737 O 0 0 0 0 0 0 0 0 0 0 0 0 8.1582 1.9873 -2.9765 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6452 -1.5194 0.3920 C 0 0 1 0 0 0 0 0 0 0 0 0 1.2429 -2.5530 1.4088 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2594 -2.5580 1.2844 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9758 -3.2663 1.9421 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6331 -1.5843 0.2594 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4815 -2.2534 -1.1085 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9441 -0.9329 0.3786 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0652 0.2343 -0.2339 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9078 0.7946 -0.9720 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1413 1.5745 -1.9300 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4984 0.4689 -0.6213 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5105 -0.5644 0.4511 C 0 0 2 0 0 0 0 0 0 0 0 0 0.2579 0.0155 1.8238 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3835 0.9115 -0.1951 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5262 1.5774 1.1522 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4996 2.0041 -1.2279 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9034 2.5638 -1.0480 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9463 1.5562 -1.3928 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.7330 0.1929 -0.8742 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7454 -0.1131 0.2434 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1627 -0.7777 -1.9947 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3943 -0.1950 -0.4034 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.4039 -0.9335 0.9166 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0411 -1.5449 1.1280 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8058 -1.6087 2.5138 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.1779 2.0385 -0.9189 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3362 -3.2397 0.3209 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7483 -2.3614 0.8746 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2436 -2.3663 -0.8968 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1861 -0.4159 -0.4989 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5895 -1.1189 2.4367 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9588 0.4574 1.9790 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7504 -0.6162 -0.3707 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2186 1.0640 -0.4019 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6886 0.1708 1.1589 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1404 2.1485 2.2653 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9743 2.8203 0.8542 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1935 2.7930 0.8970 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5547 1.6296 -3.8481 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0539 1.3354 -2.9368 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5191 3.0238 -3.1211 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5198 -2.0618 -0.6032 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6067 -2.3920 2.4171 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5186 -3.6036 1.1056 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0570 -3.2746 -1.0245 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0166 -1.6093 -1.8579 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5422 -2.4206 -1.4649 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0689 0.0797 -1.4830 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9940 1.3952 -0.2628 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8245 0.1616 2.0210 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6633 1.0610 1.9026 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6227 -0.6294 2.6409 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5893 1.7738 1.4136 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9997 1.0630 1.9643 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0587 2.6036 1.0850 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8256 2.8235 -0.9421 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4307 1.6580 -2.2630 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0523 3.0627 -0.0767 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9647 3.4049 -1.8007 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0579 1.5746 -2.5180 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9948 -1.1949 0.2657 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4413 0.2639 1.2141 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6994 0.3697 -0.1267 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2485 -0.8690 -2.0195 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8365 -0.3218 -2.9503 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6207 -1.7406 -1.8988 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9265 -0.8980 -1.1391 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5560 -0.2310 1.7721 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1561 -1.7417 0.9227 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1639 -2.6443 0.8482 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3426 -2.2966 2.9456 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1071 2.3381 0.0281 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 4 6 1 0 6 7 1 0 7 8 1 0 7 9 1 0 9 10 2 0 9 11 1 0 11 12 1 0 2 13 1 0 13 14 1 0 14 15 1 0 15 16 2 0 15 17 1 0 17 18 1 6 17 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 21 23 1 0 23 24 1 0 24 25 1 1 20 26 1 0 26 27 1 1 26 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 31 33 1 0 31 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 30 38 1 0 24 13 1 0 34 26 1 0 24 17 1 0 36 19 1 0 1 39 1 0 1 40 1 0 1 41 1 0 2 42 1 6 3 43 1 0 3 44 1 0 6 45 1 0 6 46 1 0 7 47 1 0 8 48 1 0 8 49 1 0 8 50 1 0 12 51 1 0 12 52 1 0 12 53 1 0 13 54 1 6 14 55 1 0 14 56 1 0 18 57 1 0 18 58 1 0 18 59 1 0 23 60 1 0 23 61 1 0 25 62 1 0 25 63 1 0 25 64 1 0 27 65 1 0 27 66 1 0 27 67 1 0 28 68 1 0 28 69 1 0 29 70 1 0 29 71 1 0 30 72 1 6 32 73 1 0 32 74 1 0 32 75 1 0 33 76 1 0 33 77 1 0 33 78 1 0 34 79 1 6 35 80 1 0 35 81 1 0 36 82 1 6 37 83 1 0 38 84 1 0 M END

Standard InCHIKey	RDZRNUXQSVYSHW-DEPVCMHBSA-N
Standard InCHI	InChI=1S/C31H46O7/c1-16(11-18(32)12-17(2)27(37)38-8)19-13-24(36)31(7)26-20(33)14-22-28(3,4)23(35)9-10-29(22,5)25(26)21(34)15-30(19,31)6/h16-17,19-20,22-23,33,35H,9-15H2,1-8H3/t16-,17?,19-,20+,22+,23+,29+,30-,31+/m1/s1
SMILES	C[C@H](CC(=O)CC(C)C(=O)OC)[C@H]1CC(=O)[C@@]2(C)C3=C(C(=O)C[C@]12C)[C@@]1(C)CC[C@@H](C(C)(C)[C@@H]1C[C@@H]3O)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
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/j.phytochem.2005.10.025]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	fruit body	n.a.	PMID[11520245]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12045343]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[14695801]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1791484]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	spore	n.a.	PMID[18827358]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	fruiting bodies	Nagano, Japan	2008-MAY	PMID[20039640]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20384295]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	fruiting bodies	n.a.	n.a.	PMID[20702092]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	fruiting bodies	n.a.	n.a.	PMID[21924611]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22014750]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	fruit body	n.a.	PMID[22044278]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	fruiting body	n.a.	n.a.	PMID[22047696]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26222905]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	fruit body	n.a.	PMID[9635497]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO16609	Ganoderma sinense	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16609	Ganoderma sinense	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO16609	Ganoderma sinense	Species	Ganodermataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25269	Ganoderma lucidum	Species	Ganodermataceae	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

Activity Type	# Activity
Inhibition	1

Activity Type	# Activity
Cell line	1

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
NPT520	Cell line	3T3-L1	Mus musculus	Inhibition	=	22.0	%	PMID[20039640]

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 NPC144660 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	19088
0.1-0.2	27718
0.2-0.3	2882
0.3-0.4	99
0.4-0.5	40
0.5-0.6	18
0.6-0.7	7
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8235	Intermediate Similarity	NPC281702
0.7879	Intermediate Similarity	NPC106557
0.7727	Intermediate Similarity	NPC28656
0.7246	Intermediate Similarity	NPC600026
0.7143	Intermediate Similarity	NPC16021
0.6714	Remote Similarity	NPC122294
0.6667	Remote Similarity	NPC307954
0.6562	Remote Similarity	NPC297199
0.6351	Remote Similarity	NPC293753
0.6301	Remote Similarity	NPC205899
0.6056	Remote Similarity	NPC3772
0.6027	Remote Similarity	NPC135854
0.5972	Remote Similarity	NPC470254
0.5942	Remote Similarity	NPC469561
0.5676	Remote Similarity	NPC77947
0.5541	Remote Similarity	NPC255809
0.5467	Remote Similarity	NPC125622
0.5455	Remote Similarity	NPC243525
0.5455	Remote Similarity	NPC55872
0.5455	Remote Similarity	NPC40765
0.5395	Remote Similarity	NPC264404
0.5375	Remote Similarity	NPC115303
0.5256	Remote Similarity	NPC51452
0.525	Remote Similarity	NPC21358
0.525	Remote Similarity	NPC234892
0.5244	Remote Similarity	NPC56498
0.519	Remote Similarity	NPC121339
0.5128	Remote Similarity	NPC7124
0.5065	Remote Similarity	NPC37646
0.5063	Remote Similarity	NPC286174

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC144660 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7048
0.1-0.2	2064
0.2-0.3	38
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