NPASS Compound

Natural Product: NPC255309

Natural Product ID	NPC255309
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Paraminabeolide D
IUPAC Name	(3R,4S,5R)-5-[(1S,2S)-2-[(8S,9S,10R,13S,14S,17R)-10,13-dimethyl-3-oxo-6,7,8,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthren-17-yl]-1-hydroxypropyl]-3,4-dimethyloxolan-2-one
Synonyms	Paraminabeolide D
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL1782225
PubChem CID	53262738
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001125] Steroid lactones [CHEMONTID:0001560] Withanolides and derivatives

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 72 76 0 0 0 0 0 0 0 0999 V2000 -4.5051 1.0729 1.2568 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0650 -0.3049 1.0963 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.4855 -0.1756 0.5923 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.2182 1.0081 1.1753 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2346 0.1099 -0.8585 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1019 0.4835 -1.7087 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8705 -0.1022 -1.1398 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4116 -0.9627 -0.1297 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.9173 -0.9091 0.1152 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1008 -1.3907 -1.0341 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3395 -0.5757 -2.3079 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6547 -1.6129 -0.7853 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0802 -2.1275 -2.1217 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1396 -1.2766 -2.4045 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5205 -0.9280 -1.0202 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5790 0.1077 -0.8552 C 0 0 2 0 0 0 0 0 0 0 0 0 3.6961 -0.0235 -1.8267 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6725 1.1389 -1.5761 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1486 0.8803 -0.1651 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4143 0.6787 0.0356 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9948 0.4086 1.3542 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2044 0.2204 1.5316 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0553 0.3733 2.4622 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7669 0.5893 2.2092 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1687 0.8712 0.9169 C 0 0 1 0 0 0 0 0 0 0 0 0 3.6243 2.3233 1.0505 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0085 -0.0268 0.6178 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7914 0.2978 1.4404 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6111 -0.5390 1.1200 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2152 -0.5024 -0.3581 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0871 0.8649 -0.8360 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7347 -1.8460 1.1751 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2569 1.7839 1.6030 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1765 1.4199 0.2335 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6621 1.1222 1.9759 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9813 -0.9411 1.9881 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0620 -1.1124 0.7203 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3061 0.7983 1.0377 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0712 1.1322 2.2573 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0144 1.9230 0.5849 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7803 -1.9959 -0.2383 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6915 0.0561 0.5375 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5175 -2.4001 -1.2789 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3768 -0.2594 -2.7718 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8642 -1.1549 -3.0969 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9077 0.3372 -2.1542 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5336 -2.4477 -0.0683 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8106 -2.1778 -2.9178 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3155 -3.1677 -2.0027 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9803 -0.4499 -3.0867 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9749 -1.8989 -2.8362 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8518 -1.8537 -0.4973 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1943 1.1433 -0.9485 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2858 0.0367 -2.8358 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2697 -0.9694 -1.6494 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1002 2.0655 -1.5606 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4637 1.1111 -2.3094 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1221 0.7059 -0.8180 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3889 0.1736 3.4920 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1395 0.5321 3.1348 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5290 2.9950 0.9771 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9714 2.5937 0.2280 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2400 2.4473 2.0649 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2434 -1.0931 0.7712 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5950 1.3856 1.5068 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0788 0.0199 2.5006 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2305 -0.2640 1.7763 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8625 -1.5985 1.3356 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1191 1.1845 -0.8627 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4068 1.5926 -0.1224 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3595 1.1027 -1.8327 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8148 -2.0030 1.4035 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 3 5 1 0 5 6 2 0 5 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 10 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 2 0 20 21 1 0 21 22 2 0 21 23 1 0 23 24 2 0 24 25 1 0 25 26 1 1 25 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 1 6 9 32 1 0 8 2 1 0 30 12 1 0 30 15 1 0 27 16 1 0 25 19 1 0 1 33 1 0 1 34 1 0 1 35 1 0 2 36 1 1 3 37 1 6 4 38 1 0 4 39 1 0 4 40 1 0 8 41 1 6 9 42 1 1 10 43 1 6 11 44 1 0 11 45 1 0 11 46 1 0 12 47 1 1 13 48 1 0 13 49 1 0 14 50 1 0 14 51 1 0 15 52 1 1 16 53 1 1 17 54 1 0 17 55 1 0 18 56 1 0 18 57 1 0 20 58 1 0 23 59 1 0 24 60 1 0 26 61 1 0 26 62 1 0 26 63 1 0 27 64 1 6 28 65 1 0 28 66 1 0 29 67 1 0 29 68 1 0 31 69 1 0 31 70 1 0 31 71 1 0 32 72 1 0 M END

Standard InCHIKey	UISXVQNCBCKQHL-PPGQKZPJSA-N
Standard InCHI	InChI=1S/C28H40O4/c1-15-16(2)26(31)32-25(15)24(30)17(3)21-8-9-22-20-7-6-18-14-19(29)10-12-27(18,4)23(20)11-13-28(21,22)5/h10,12,14-17,20-25,30H,6-9,11,13H2,1-5H3/t15-,16+,17-,20-,21+,22-,23-,24-,25+,27-,28+/m0/s1
SMILES	C[C@H]1[C@@H](C)C(=O)O[C@H]1[C@H]([C@@H](C)[C@H]1CC[C@H]2[C@@H]3CCC4=CC(=O)C=C[C@]4(C)[C@H]3CC[C@]12C)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
NPO27202	Paraminabea acronocephala	Species	Alcyoniidae	Eukaryota	n.a.	the western coast of Pingtung county, Taiwan, at a depth of 10 m	2009-MAY	PMID[21425785]
NPO27202	Paraminabea acronocephala	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	PMID[21425785]
NPO27202	Paraminabea acronocephala	Species	Alcyoniidae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27202	Paraminabea acronocephala	Species	Alcyoniidae	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
NPT113	Cell line	RAW264.7	Mus musculus	Inhibition	=	43.3	%	PMID[21425785]

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 NPC255309 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	17060
0.1-0.2	25823
0.2-0.3	6777
0.3-0.4	165
0.4-0.5	8
0.5-0.6	13
0.6-0.7	9
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
0.8095	Intermediate Similarity	NPC96377
0.6719	Remote Similarity	NPC608739
0.6562	Remote Similarity	NPC218301
0.6491	Remote Similarity	NPC92327
0.6418	Remote Similarity	NPC164835
0.6418	Remote Similarity	NPC228669
0.6308	Remote Similarity	NPC273199
0.6286	Remote Similarity	NPC601481
0.6094	Remote Similarity	NPC474463
0.6032	Remote Similarity	NPC105197
0.589	Remote Similarity	NPC471398
0.589	Remote Similarity	NPC604986
0.5873	Remote Similarity	NPC176107
0.5857	Remote Similarity	NPC177141
0.5806	Remote Similarity	NPC6434
0.5694	Remote Similarity	NPC58052
0.5588	Remote Similarity	NPC190211
0.5556	Remote Similarity	NPC111684
0.5429	Remote Similarity	NPC470923
0.5352	Remote Similarity	NPC310981
0.5342	Remote Similarity	NPC281134
0.5323	Remote Similarity	NPC54123
0.527	Remote Similarity	NPC600537

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC255309 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6354
0.1-0.2	2456
0.2-0.3	268
0.3-0.4	57
0.4-0.5	14
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
0.5312	Remote Similarity	NPD4195	Phase 4

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