NPASS Compound

Natural Product: NPC606508

Natural Product ID	NPC606508
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	AIFSZKWYZWWHDQ-PAEBMLBLSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL525629
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 81 85 0 0 0 0 0 0 0 0999 V2000 7.4457 -0.7052 -1.6522 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9349 -0.0365 -0.4411 C 0 0 0 0 0 0 0 0 0 0 0 0 9.4401 0.0199 -0.2345 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2076 0.5161 0.4810 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7686 0.6182 0.5596 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3725 1.2370 1.6383 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7598 0.1263 -0.3931 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4038 0.4974 0.1700 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4365 2.0081 0.2458 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2463 -0.0395 -0.6060 C 0 0 1 0 0 0 0 0 0 0 0 0 2.2621 -1.5543 -0.7220 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8499 -2.0617 -0.5015 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0683 -0.8038 -0.8259 C 0 0 1 0 0 0 0 0 0 0 0 0 0.2251 -0.6926 -2.3107 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3652 -0.8032 -0.5137 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2515 -0.3186 -1.6767 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6515 -0.8592 -1.3270 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1616 0.1259 -0.3347 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.5643 -0.1497 0.1340 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9272 -1.5621 -0.2719 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5623 0.7812 -0.5365 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2966 2.1147 -0.2677 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7239 -0.0131 1.6103 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.4147 -1.2169 2.2822 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0229 1.1566 2.2063 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7105 1.4997 1.5786 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2383 0.2569 0.8055 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6852 -0.7754 1.6292 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8226 -0.0081 0.6580 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9508 1.0979 1.0970 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2261 1.3711 0.1462 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9173 0.1154 0.0145 C 0 0 2 0 0 0 0 0 0 0 0 0 1.0549 -0.4940 1.4208 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8047 -0.0595 -2.2650 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3205 -0.9346 -2.3469 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9281 -1.6272 -1.3848 H 0 0 0 0 0 0 0 0 0 0 0 0 9.9489 -0.6889 -0.9116 H 0 0 0 0 0 0 0 0 0 0 0 0 9.7971 1.0617 -0.3503 H 0 0 0 0 0 0 0 0 0 0 0 0 9.6480 -0.2776 0.8128 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8188 0.9663 1.3161 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8414 0.6640 -1.3756 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9013 -0.9242 -0.5572 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3630 0.1070 1.1922 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4217 2.4490 -0.0552 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7665 2.3663 -0.5943 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0498 2.4373 1.1653 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2570 0.4904 -1.5726 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9102 -2.0616 -0.0096 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6649 -1.8707 -1.7313 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6567 -2.4873 0.4740 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6678 -2.8513 -1.2877 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2372 0.2086 -2.7498 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2549 -0.8066 -2.7046 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2400 -1.6532 -2.7117 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6643 -1.8951 -0.4222 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0266 -0.7432 -2.6351 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2602 0.7812 -1.7268 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5382 -1.8805 -0.9651 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2518 -0.7958 -2.2758 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1936 1.1234 -0.8584 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8911 -1.6099 -1.3745 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2467 -2.2890 0.2126 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9683 -1.7382 0.0535 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3890 0.6530 -1.6450 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5951 0.4902 -0.3576 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0467 2.5017 0.2562 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8275 0.1310 1.8057 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1599 -1.8439 2.0459 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6475 2.0919 2.1766 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9223 0.9451 3.3120 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7356 2.3887 0.9362 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9835 1.6592 2.4290 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8794 -1.8613 1.4378 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4257 -0.5856 2.6871 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4801 2.0974 1.1362 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6119 0.9155 2.1331 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2443 1.7567 -0.7843 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8001 2.1731 0.5945 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8745 -1.2206 1.4930 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3360 0.3245 2.1485 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1646 -0.9954 1.7721 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 2 3 4 5 1 0 5 6 2 0 5 7 1 0 7 8 1 0 8 9 1 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 6 13 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 6 19 21 1 0 21 22 1 0 19 23 1 0 23 24 1 0 23 25 1 0 25 26 1 0 27 26 1 1 27 28 1 0 29 28 1 1 29 30 1 0 30 31 1 0 31 32 1 0 32 33 1 1 32 10 1 0 32 13 1 0 29 15 1 0 27 18 1 0 29 27 1 0 1 34 1 0 1 35 1 0 1 36 1 0 3 37 1 0 3 38 1 0 3 39 1 0 4 40 1 0 7 41 1 0 7 42 1 0 8 43 1 1 9 44 1 0 9 45 1 0 9 46 1 0 10 47 1 6 11 48 1 0 11 49 1 0 12 50 1 0 12 51 1 0 14 52 1 0 14 53 1 0 14 54 1 0 15 55 1 1 16 56 1 0 16 57 1 0 17 58 1 0 17 59 1 0 18 60 1 6 20 61 1 0 20 62 1 0 20 63 1 0 21 64 1 0 21 65 1 0 22 66 1 0 23 67 1 6 24 68 1 0 25 69 1 0 25 70 1 0 26 71 1 0 26 72 1 0 28 73 1 0 28 74 1 0 30 75 1 0 30 76 1 0 31 77 1 0 31 78 1 0 33 79 1 0 33 80 1 0 33 81 1 0 M END

Standard InCHIKey	AIFSZKWYZWWHDQ-PAEBMLBLSA-N
Standard InCHI	InChI=1S/C30H48O3/c1-19(2)15-21(32)16-20(3)22-9-11-28(6)24-8-7-23-26(4,18-31)25(33)10-12-29(23)17-30(24,29)14-13-27(22,28)5/h15,20,22-25,31,33H,7-14,16-18H2,1-6H3/t20-,22-,23+,24+,25+,26+,27-,28+,29-,30+/m1/s1
SMILES	CC(C)=CC(=O)C[C@@H](C)[C@H]1CC[C@@]2(C)[C@@H]3CC[C@H]4[C@](C)(CO)[C@@H](O)CC[C@@]45C[C@@]35CC[C@]12C

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
NPO52	Tydemania expeditionis	Species	Udoteaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8158167]
NPO52	Tydemania expeditionis	Species	Udoteaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO52	Tydemania expeditionis	Species	Udoteaceae	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
IC50	12
Activity	1

Activity Type	# Activity
Cell line	10
Non-molecular	2
Organism	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
NPT90	Cell line	DU-145	Homo sapiens	IC50	=	6000.0	nM	PMID[18763828]
NPT82	Cell line	MDA-MB-231	Homo sapiens	IC50	=	6000.0	nM	PMID[18763828]
NPT2155	Cell line	SHP77	Homo sapiens	IC50	=	6000.0	nM	PMID[18763828]
NPT393	Cell line	HCT-116	Homo sapiens	IC50	=	6000.0	nM	PMID[18763828]
NPT937	Cell line	NCI-H446	Homo sapiens	IC50	=	6000.0	nM	PMID[18763828]
NPT784	Cell line	MDA-MB-468	Homo sapiens	IC50	=	6000.0	nM	PMID[18763828]
NPT306	Cell line	PC-3	Homo sapiens	IC50	=	6000.0	nM	PMID[18763828]
NPT1900	Cell line	DU-4475	Homo sapiens	IC50	=	6000.0	nM	PMID[18763828]
NPT404	Cell line	CCRF-CEM	Homo sapiens	IC50	=	6000.0	nM	PMID[18763828]
NPT457	Cell line	BT-549	Homo sapiens	IC50	=	6000.0	nM	PMID[18763828]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	=	6000.0	nM	PMID[18763828]
NPT3927	Organism	Rotifers	Rotifera	Activity	=	9.0	%	PMID[18763828]

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 NPC606508 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	18182
0.1-0.2	27397
0.2-0.3	3785
0.3-0.4	364
0.4-0.5	65
0.5-0.6	53
0.6-0.7	6
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
0.7213	Intermediate Similarity	NPC603266
0.6462	Remote Similarity	NPC486363
0.6316	Remote Similarity	NPC22133
0.6308	Remote Similarity	NPC603267
0.6286	Remote Similarity	NPC239293
0.6102	Remote Similarity	NPC12722
0.6	Remote Similarity	NPC89747
0.5965	Remote Similarity	NPC85346
0.5965	Remote Similarity	NPC65897
0.5965	Remote Similarity	NPC80237
0.5938	Remote Similarity	NPC486365
0.5932	Remote Similarity	NPC76518
0.5932	Remote Similarity	NPC483442
0.5932	Remote Similarity	NPC69408
0.5893	Remote Similarity	NPC607543
0.5862	Remote Similarity	NPC273366
0.5735	Remote Similarity	NPC312900
0.569	Remote Similarity	NPC82623
0.569	Remote Similarity	NPC604180
0.5667	Remote Similarity	NPC472341
0.5606	Remote Similarity	NPC488976
0.5606	Remote Similarity	NPC37153
0.5593	Remote Similarity	NPC472342
0.5571	Remote Similarity	NPC486361
0.5556	Remote Similarity	NPC18384
0.5517	Remote Similarity	NPC331618
0.5517	Remote Similarity	NPC257191
0.5517	Remote Similarity	NPC196358
0.55	Remote Similarity	NPC302041
0.5484	Remote Similarity	NPC134481
0.5439	Remote Similarity	NPC41577
0.5429	Remote Similarity	NPC486370
0.5429	Remote Similarity	NPC486371
0.5429	Remote Similarity	NPC486372
0.5424	Remote Similarity	NPC200243
0.5424	Remote Similarity	NPC254509
0.541	Remote Similarity	NPC67872
0.5385	Remote Similarity	NPC1015
0.5362	Remote Similarity	NPC478129
0.5345	Remote Similarity	NPC299948
0.5345	Remote Similarity	NPC241085
0.5333	Remote Similarity	NPC470830
0.5333	Remote Similarity	NPC195530
0.5333	Remote Similarity	NPC479659
0.5323	Remote Similarity	NPC477858
0.5286	Remote Similarity	NPC124207
0.5286	Remote Similarity	NPC81256
0.5231	Remote Similarity	NPC307776
0.5205	Remote Similarity	NPC486367
0.5161	Remote Similarity	NPC282275
0.5156	Remote Similarity	NPC479660
0.5152	Remote Similarity	NPC195366
0.5152	Remote Similarity	NPC60350
0.5152	Remote Similarity	NPC114743
0.5082	Remote Similarity	NPC145552
0.5082	Remote Similarity	NPC214770
0.5082	Remote Similarity	NPC477856
0.5077	Remote Similarity	NPC475740
0.5077	Remote Similarity	NPC110923
0.5077	Remote Similarity	NPC74296

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC606508 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6855
0.1-0.2	2120
0.2-0.3	171
0.3-0.4	4
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