NPASS Compound

Natural Product: NPC471970

Natural Product ID	NPC471970
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	CUGYULTVVPEDBO-VZXWCEDBSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3314597
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001549] Monoterpenoids [CHEMONTID:0001564] Bicyclic monoterpenoids

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 101103 0 0 0 0 0 0 0 0999 V2000 -5.2959 -4.7076 2.9385 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2474 -4.1779 2.2476 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2630 -2.8208 2.0930 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0000 -2.4182 1.2868 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.0909 -0.9196 1.0961 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9568 -0.3625 0.3170 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6586 -0.6301 1.0247 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5223 -0.0685 0.1877 C 0 0 2 0 0 0 0 0 0 0 0 0 1.4300 -1.1874 -0.1157 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1488 -1.9334 0.8959 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1982 -1.3247 1.7047 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9347 -0.2897 1.3016 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5412 -1.8192 3.0899 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4520 -3.3524 0.4899 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2521 -3.4817 -0.7379 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4752 -3.9717 -0.6793 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1015 -4.4099 0.5922 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2963 -4.1095 -1.9387 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9879 1.0816 0.9459 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9955 2.3042 0.3307 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2468 2.6540 -0.3946 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5809 3.8446 -0.4833 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0720 1.5292 -1.0011 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1317 1.1328 -0.0319 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5539 1.2545 -0.5517 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1113 1.9400 1.2434 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1237 0.3746 -1.1145 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1379 -0.1921 -2.1348 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4895 2.0590 -2.3184 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2511 1.2457 -3.2383 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7971 1.0515 -4.4637 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5277 1.6552 -4.9019 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5675 0.2172 -5.4097 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1168 3.1612 0.5501 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9973 2.7866 1.4382 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4348 4.4106 -0.0790 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9298 4.9246 -1.2327 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2154 6.1717 -1.7367 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0772 6.9858 -1.0465 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6243 6.5293 0.1212 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3217 5.2780 0.6056 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5085 7.3510 0.8335 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3869 8.2630 -1.5378 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4143 1.0006 2.2484 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1134 -3.0984 0.0760 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1684 -2.0451 3.3730 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4152 -2.4106 1.2307 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4266 -4.3546 3.9776 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0996 -5.8238 3.0710 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2757 -4.7186 2.3757 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1080 -2.7597 1.8095 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0952 -0.7144 0.7289 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0905 -0.5073 2.1560 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8667 -0.8503 -0.6852 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5532 -1.7178 1.1019 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6860 -0.2156 2.0319 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2190 -0.7988 -0.8629 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9058 -1.9582 -0.7868 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3026 -2.1895 1.7480 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7172 0.1104 0.2940 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7079 0.1782 1.8634 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6304 -1.8793 3.2265 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1351 -1.1428 3.8622 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0640 -2.8340 3.2068 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9726 -3.9129 1.3040 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4809 -3.9371 0.3745 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8619 -3.1842 -1.6987 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9865 -3.6714 1.4141 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7456 -5.4120 0.9233 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2102 -4.5100 0.4402 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4480 -5.1913 -2.1471 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8089 -3.5981 -2.7695 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2686 -3.6189 -1.7272 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9678 0.3384 -0.9656 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2005 1.4676 0.3684 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7187 2.0934 -1.2210 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0589 1.2702 2.1429 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0453 2.5864 1.3508 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2987 2.6569 1.2382 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0742 2.9967 -2.1077 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5681 2.4425 -2.8227 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1998 0.7519 -3.0383 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3540 1.4083 -4.3067 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3572 1.5061 -5.9973 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6566 2.7782 -4.8165 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2695 0.9248 -5.9422 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2592 -0.4655 -4.8310 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9583 -0.3633 -6.1108 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2890 4.2835 -1.8648 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7695 6.5165 -2.6678 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7841 4.9917 1.5211 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4375 7.3302 1.8489 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8798 8.8998 -0.9036 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8267 0.8165 3.0406 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2680 -3.1163 -0.4393 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6650 -1.0522 3.3051 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0801 -1.8962 3.6407 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5865 -2.5633 4.2567 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7938 -1.4266 1.5947 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1302 -2.3556 0.1363 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2856 -3.0846 1.2446 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 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 6 9 10 1 0 10 11 1 0 11 12 2 0 11 13 1 0 10 14 1 0 14 15 1 0 15 16 2 3 16 17 1 0 16 18 1 0 8 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 0 24 26 1 0 23 27 1 0 27 28 2 0 23 29 1 6 29 30 1 0 30 31 2 3 31 32 1 0 31 33 1 0 20 34 1 0 34 35 2 0 34 36 1 0 36 37 2 0 37 38 1 0 38 39 2 0 39 40 1 0 40 41 2 0 40 42 1 0 39 43 1 0 19 44 1 0 4 45 1 0 3 46 1 0 3 47 1 0 24 6 1 0 41 36 1 0 27 8 1 0 1 48 1 0 1 49 1 0 1 50 1 0 4 51 1 1 5 52 1 0 5 53 1 0 6 54 1 6 7 55 1 0 7 56 1 0 9 57 1 0 9 58 1 0 10 59 1 0 12 60 1 0 12 61 1 0 13 62 1 0 13 63 1 0 13 64 1 0 14 65 1 0 14 66 1 0 15 67 1 0 17 68 1 0 17 69 1 0 17 70 1 0 18 71 1 0 18 72 1 0 18 73 1 0 25 74 1 0 25 75 1 0 25 76 1 0 26 77 1 0 26 78 1 0 26 79 1 0 29 80 1 0 29 81 1 0 30 82 1 0 32 83 1 0 32 84 1 0 32 85 1 0 33 86 1 0 33 87 1 0 33 88 1 0 37 89 1 0 38 90 1 0 41 91 1 0 42 92 1 0 43 93 1 0 44 94 1 0 45 95 1 0 46 96 1 0 46 97 1 0 46 98 1 0 47 99 1 0 47100 1 0 47101 1 0 M END

Standard InCHIKey	CUGYULTVVPEDBO-VZXWCEDBSA-N
Standard InCHI	InChI=1S/C39H54O8/c1-22(2)12-13-26(24(5)6)20-38-21-27(19-30(42)37(9,10)47-11)36(7,8)39(35(38)46,17-16-23(3)4)34(45)31(33(38)44)32(43)25-14-15-28(40)29(41)18-25/h12,14-16,18,26-27,30,40-42,44H,5,13,17,19-21H2,1-4,6-11H3/t26?,27-,30+,38-,39+/m1/s1
SMILES	COC([C@H](C[C@@H]1C[C@]2(CC(C(=C)C)CC=C(C)C)C(=C(C(=O)[C@](C1(C)C)(C2=O)CC=C(C)C)C(=O)c1ccc(c(c1)O)O)O)O)(C)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
NPO32711	garcinia esculenta	Species	Clusiaceae	Eukaryota	twigs	n.a.	n.a.	PMID[24960143]

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

Activity Type	# Activity
Cell line	4

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
NPT65	Cell line	HepG2	Homo sapiens	IC50	>	10000.0	nM	DOI[10.1016/j.cropro.2012.04.001]
NPT83	Cell line	MCF7	Homo sapiens	IC50	>	10000.0	nM	PMID[22037378]
NPT82	Cell line	MDA-MB-231	Homo sapiens	IC50	>	10000.0	nM	PMID[18163588]
NPT113	Cell line	RAW264.7	Mus musculus	IC50	=	24900.0	nM	DrugMatrix in vitro pharmacology data

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 NPC471970 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	5249
0.1-0.2	41591
0.2-0.3	2916
0.3-0.4	24
0.4-0.5	26
0.5-0.6	14
0.6-0.7	18
0.7-0.8	0
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8493	Intermediate Similarity	NPC469856
0.8429	Intermediate Similarity	NPC46242
0.8429	Intermediate Similarity	NPC91887
0.8429	Intermediate Similarity	NPC93556
0.7867	Intermediate Similarity	NPC471971
0.7867	Intermediate Similarity	NPC471972
0.7867	Intermediate Similarity	NPC469855
0.76	Intermediate Similarity	NPC469857
0.76	Intermediate Similarity	NPC245760
0.7403	Intermediate Similarity	NPC469854
0.7333	Intermediate Similarity	NPC297797
0.7273	Intermediate Similarity	NPC294330
0.7222	Intermediate Similarity	NPC149773
0.6875	Remote Similarity	NPC237441
0.6709	Remote Similarity	NPC30846
0.6625	Remote Similarity	NPC479151
0.6543	Remote Similarity	NPC603871
0.65	Remote Similarity	NPC165191
0.65	Remote Similarity	NPC177501
0.6375	Remote Similarity	NPC114333
0.6375	Remote Similarity	NPC28592
0.6375	Remote Similarity	NPC51531
0.6296	Remote Similarity	NPC473479
0.6296	Remote Similarity	NPC50615
0.6296	Remote Similarity	NPC141650
0.6296	Remote Similarity	NPC479148
0.6203	Remote Similarity	NPC289358
0.6203	Remote Similarity	NPC4289
0.6203	Remote Similarity	NPC42384
0.619	Remote Similarity	NPC479146
0.6024	Remote Similarity	NPC482621
0.5823	Remote Similarity	NPC473779
0.5765	Remote Similarity	NPC5014
0.5663	Remote Similarity	NPC473527
0.5647	Remote Similarity	NPC23667
0.5647	Remote Similarity	NPC157284
0.5618	Remote Similarity	NPC482617
0.5618	Remote Similarity	NPC482616
0.5584	Remote Similarity	NPC259400
0.5584	Remote Similarity	NPC130591
0.5584	Remote Similarity	NPC234637
0.5443	Remote Similarity	NPC611064
0.5333	Remote Similarity	NPC482618
0.5294	Remote Similarity	NPC198803
0.5176	Remote Similarity	NPC479147

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC471970 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3213
0.1-0.2	5879
0.2-0.3	58
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