NPASS Compound

Natural Product: NPC572740

Natural Product ID	NPC572740
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Cholest-4-en-3-one
IUPAC Name	(8~{S},9~{S},10~{R},13~{S},14~{R},17~{R})-17-[(1~{R})-1,5-dimethylhexyl]-10,13-dimethyl-1,2,6,7,8,9,11,12,14,15,16,17-dodecahydrocyclopenta[a]phenanthren-3-one
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 75 0 0 0 0 0 0 0 0999 V2000 7.3761 -0.2358 1.2002 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8786 -0.1823 0.8838 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4128 -1.6204 0.8105 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7563 0.4801 -0.4486 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3082 0.6158 -0.9238 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4919 1.4272 0.0211 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0459 1.6165 -0.3852 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0926 2.3051 -1.7076 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3714 0.3307 -0.3142 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4637 -0.1983 1.1303 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4036 -1.3195 1.0090 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6788 -0.4374 0.4641 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.0222 -0.9571 0.3425 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2942 -2.2429 -0.3248 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7807 -2.4890 -0.3668 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6267 -1.3943 0.0718 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8966 -1.6545 0.3659 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7312 -0.5278 0.8071 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6422 -0.7301 1.6647 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5328 0.8263 0.2758 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1947 0.9799 -0.4211 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2163 0.0384 0.2366 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1912 0.2966 1.7295 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8519 0.1193 -0.3793 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.2226 1.4642 -0.2779 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8244 1.5252 -0.8621 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0647 0.2442 -0.7176 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0936 -0.4929 -2.0091 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7789 -1.0850 0.6124 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4765 -0.3610 2.2897 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8646 0.6852 0.8127 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3295 0.3011 1.6892 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3732 -1.7272 0.4825 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4869 -2.0262 1.8446 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1012 -2.2315 0.1823 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3020 1.4329 -0.5226 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2415 -0.1962 -1.2127 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9748 -0.4293 -1.0731 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3811 1.0542 -1.9410 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9492 2.4636 0.0169 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5563 1.0451 1.0427 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6166 2.3373 0.3629 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2066 2.8128 -2.0510 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8990 3.0952 -1.6281 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4456 1.6475 -2.5364 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9898 -0.4195 -0.8661 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4402 -0.6129 1.3661 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1820 0.5497 1.8655 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7704 -2.0714 0.3157 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2094 -1.6590 2.0313 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7373 0.3892 1.2554 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4359 -1.0738 1.3954 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7977 -3.0577 0.2704 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9240 -2.3457 -1.3568 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1207 -2.8313 -1.3890 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0248 -3.3780 0.2874 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2977 -2.6434 0.2866 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6650 1.5681 1.0645 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3034 1.0722 -0.5091 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8345 1.9993 -0.2578 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2548 0.7802 -1.4939 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9550 1.0439 2.0383 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2128 0.6784 2.0853 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3998 -0.6119 2.3313 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0053 -0.1354 -1.4467 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8955 2.1645 -0.8561 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2355 1.8705 0.7542 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9589 1.7868 -1.9311 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3104 2.3406 -0.2828 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9648 -0.4081 -2.6347 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2723 -1.5541 -1.8678 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7498 -0.0465 -2.6297 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 0 7 8 1 0 7 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 18 20 1 0 20 21 1 0 21 22 1 0 22 23 1 1 22 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 6 27 9 1 0 27 12 1 0 24 13 1 0 22 16 1 0 1 29 1 0 1 30 1 0 1 31 1 0 2 32 1 0 3 33 1 0 3 34 1 0 3 35 1 0 4 36 1 0 4 37 1 0 5 38 1 0 5 39 1 0 6 40 1 0 6 41 1 0 7 42 1 1 8 43 1 0 8 44 1 0 8 45 1 0 9 46 1 6 10 47 1 0 10 48 1 0 11 49 1 0 11 50 1 0 12 51 1 1 13 52 1 1 14 53 1 0 14 54 1 0 15 55 1 0 15 56 1 0 17 57 1 0 20 58 1 0 20 59 1 0 21 60 1 0 21 61 1 0 23 62 1 0 23 63 1 0 23 64 1 0 24 65 1 6 25 66 1 0 25 67 1 0 26 68 1 0 26 69 1 0 28 70 1 0 28 71 1 0 28 72 1 0 M END

Standard InCHIKey	NYOXRYYXRWJDKP-GAMCMBBHSA-N
Standard InCHI	InChI=1S/C27H44O/c1-18(2)7-6-8-19(3)23-11-12-24-22-10-9-20-17-21(28)13-15-26(20,4)25(22)14-16-27(23,24)5/h17-19,22-25H,6-16H2,1-5H3/t19-,22+,23-,24-,25+,26+,27+/m1/s1
SMILES	CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@H]3CCC4=CC(=O)CC[C@]4(C)[C@H]3CC[C@]21C

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
NPO55506	Streptomyces FX-58	Genus	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]
NPO47228	Streptomyces thermophilus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[COCONUT]

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 NPC572740 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	20739
0.1-0.2	25473
0.2-0.3	3355
0.3-0.4	206
0.4-0.5	43
0.5-0.6	26
0.6-0.7	4
0.7-0.8	3
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC35734
0.8125	Intermediate Similarity	NPC282593
0.7959	Intermediate Similarity	NPC159577
0.7959	Intermediate Similarity	NPC602429
0.78	Intermediate Similarity	NPC149203
0.7593	Intermediate Similarity	NPC320514
0.7358	Intermediate Similarity	NPC469948
0.7308	Intermediate Similarity	NPC249312
0.7143	Intermediate Similarity	NPC307176
0.7143	Intermediate Similarity	NPC321874
0.7059	Intermediate Similarity	NPC214043
0.7059	Intermediate Similarity	NPC85774
0.6923	Remote Similarity	NPC115023
0.6481	Remote Similarity	NPC237712
0.6071	Remote Similarity	NPC303613
0.6	Remote Similarity	NPC244488
0.5962	Remote Similarity	NPC139397
0.5741	Remote Similarity	NPC2634
0.5741	Remote Similarity	NPC265782
0.5741	Remote Similarity	NPC251929
0.5667	Remote Similarity	NPC309603
0.5536	Remote Similarity	NPC255021
0.5536	Remote Similarity	NPC227064
0.5536	Remote Similarity	NPC474228
0.5536	Remote Similarity	NPC329043
0.5536	Remote Similarity	NPC58841
0.5536	Remote Similarity	NPC161423
0.5517	Remote Similarity	NPC323765
0.5484	Remote Similarity	NPC305039
0.5439	Remote Similarity	NPC144258
0.5439	Remote Similarity	NPC327115
0.5417	Remote Similarity	NPC246205
0.5246	Remote Similarity	NPC153987
0.5238	Remote Similarity	NPC205860
0.5167	Remote Similarity	NPC310010
0.5167	Remote Similarity	NPC326627
0.5152	Remote Similarity	NPC187159
0.5091	Remote Similarity	NPC184819
0.5085	Remote Similarity	NPC328539
0.5082	Remote Similarity	NPC473999
0.5082	Remote Similarity	NPC31564
0.5079	Remote Similarity	NPC489872

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC572740 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6539
0.1-0.2	2343
0.2-0.3	182
0.3-0.4	51
0.4-0.5	15
0.5-0.6	16
0.6-0.7	1
0.7-0.8	3
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
0.75	Intermediate Similarity	NPD6938	Clinical (unspecified phase)
0.75	Intermediate Similarity	NPD6939	Phase 3
0.7143	Intermediate Similarity	NPD4747	Phase 4
0.614	Remote Similarity	NPD5737	Phase 4
0.5932	Remote Similarity	NPD6672	Phase 4
0.5763	Remote Similarity	NPD6409	Approved
0.5741	Remote Similarity	NPD4691	Approved
0.5536	Remote Similarity	NPD3666	Phase 4
0.5536	Remote Similarity	NPD4221	Phase 4
0.5484	Remote Similarity	NPD6904	Phase 4
0.5424	Remote Similarity	NPD5330	Phase 4
0.5397	Remote Similarity	NPD6903	Phase 4
0.5254	Remote Similarity	NPD4693	Phase 3
0.5238	Remote Similarity	NPD6083	Phase 4
0.5238	Remote Similarity	NPD6084	Phase 2
0.5238	Remote Similarity	NPD6684	Phase 4
0.5238	Remote Similarity	NPD7334	Approved
0.5238	Remote Similarity	NPD7521	Phase 4
0.5231	Remote Similarity	NPD7513	Clinical (unspecified phase)
0.5167	Remote Similarity	NPD4753	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