NPASS Compound

Natural Product: NPC608622

Natural Product ID	NPC608622
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	UYMVUDWLGIYLKY-IHRZCVOISA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL56578
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 85 89 0 0 0 0 0 0 0 0999 V2000 8.0929 -2.0202 -1.0569 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0190 -1.0868 -1.4753 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1679 -0.3150 -2.4777 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7954 -0.9877 -0.8172 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7850 -0.0790 -1.2465 C 0 0 1 0 0 0 0 0 0 0 0 0 3.6022 -0.8951 -1.7911 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9727 -1.5543 -0.5858 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3492 -0.6201 0.3866 C 0 0 1 0 0 0 0 0 0 0 0 0 2.8764 -1.0369 1.7804 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8759 0.7386 0.1202 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3855 1.7242 1.1147 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9868 1.6097 1.5362 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1666 0.4291 1.1429 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.3531 -0.1410 2.4866 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8605 -0.7000 0.4865 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1247 -1.1173 -0.7369 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6029 -1.3952 -1.8477 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.3120 -1.2141 -0.6263 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9607 -0.2193 -0.0049 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4116 -0.2668 0.1440 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.0887 -1.2450 -0.7626 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5718 -1.0530 -0.9442 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3531 -1.7447 0.1783 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9748 -1.8368 -2.2098 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0133 0.3429 -1.1608 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9764 1.3871 -0.9039 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0663 1.0544 0.2535 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.8821 1.1841 1.5135 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8944 0.2193 2.2962 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5894 2.3170 1.7997 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0937 2.2096 0.3571 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9443 1.7981 1.2598 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0914 0.8813 0.4402 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7689 1.6984 -0.8233 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3418 0.8481 -0.1299 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2677 0.6996 1.0034 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5345 2.2705 -0.6957 C 0 0 0 0 0 0 0 0 0 0 0 0 8.7588 -1.5124 -0.3212 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7356 -2.1991 -1.9536 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7333 -2.9872 -0.7050 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1870 0.4555 -2.1318 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9954 -0.1976 -2.3434 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0221 -1.7101 -2.4135 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3792 -2.4623 -0.8310 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8867 -2.0229 -0.0935 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7905 -0.2649 2.5247 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9346 -1.4018 1.6959 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3162 -1.9917 2.0079 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4193 1.0619 -0.8645 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0857 1.6809 2.0042 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6493 2.7432 0.6847 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4659 2.5237 1.1079 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9423 1.8463 2.6452 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4836 -0.7504 2.8787 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5198 0.6556 3.2180 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1909 -0.8140 2.3197 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7619 -1.6728 1.1043 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9560 -1.9970 -1.0042 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5488 -0.7332 1.1761 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6631 -1.2469 -1.8044 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9661 -2.2977 -0.4262 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8700 -0.9643 0.8019 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6993 -2.4005 0.7811 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1740 -2.3860 -0.2016 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0274 -1.5252 -2.4157 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0057 -2.9044 -1.9267 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2935 -1.6085 -3.0390 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4057 0.4775 -2.1823 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9089 0.5129 -0.4911 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3781 1.5914 -1.8148 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4942 2.3341 -0.6476 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1012 2.4852 2.6584 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6108 3.0814 0.8772 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8022 2.6149 -0.6075 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4203 1.3210 2.1324 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4783 2.7174 1.6080 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7847 2.7730 -0.6572 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5325 1.4838 -1.6351 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1690 1.4259 -1.2835 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0831 1.4891 0.9635 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8852 0.7683 2.0149 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8856 -0.2489 0.9479 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6179 2.9307 0.1910 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5061 2.3209 -1.2328 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6760 2.5078 -1.3201 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 1 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 1 13 15 1 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 2 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 22 24 1 0 22 25 1 0 25 26 1 0 26 27 1 0 27 28 1 1 28 29 2 0 28 30 1 0 27 31 1 0 31 32 1 0 32 33 1 0 33 34 1 6 10 35 1 0 35 36 1 0 35 37 1 0 35 5 1 0 15 8 1 0 33 19 1 0 33 13 1 0 27 20 1 0 1 38 1 0 1 39 1 0 1 40 1 0 5 41 1 6 6 42 1 0 6 43 1 0 7 44 1 0 7 45 1 0 9 46 1 0 9 47 1 0 9 48 1 0 10 49 1 0 11 50 1 0 11 51 1 0 12 52 1 0 12 53 1 0 14 54 1 0 14 55 1 0 14 56 1 0 15 57 1 0 18 58 1 0 20 59 1 1 21 60 1 0 21 61 1 0 23 62 1 0 23 63 1 0 23 64 1 0 24 65 1 0 24 66 1 0 24 67 1 0 25 68 1 0 25 69 1 0 26 70 1 0 26 71 1 0 30 72 1 0 31 73 1 0 31 74 1 0 32 75 1 0 32 76 1 0 34 77 1 0 34 78 1 0 34 79 1 0 36 80 1 0 36 81 1 0 36 82 1 0 37 83 1 0 37 84 1 0 37 85 1 0 M END

Standard InCHIKey	UYMVUDWLGIYLKY-IHRZCVOISA-N
Standard InCHI	InChI=1S/C32H48O5/c1-19(33)37-24-10-11-29(6)23(28(24,4)5)9-12-31(8)25(29)22(34)17-20-21-18-27(2,3)13-15-32(21,26(35)36)16-14-30(20,31)7/h17,21,23-25H,9-16,18H2,1-8H3,(H,35,36)/t21-,23?,24-,25?,29-,30+,31+,32-/m0/s1
SMILES	CC(=O)O[C@H]1CC[C@@]2(C)C(CC[C@]3(C)C2C(=O)C=C2[C@@H]4CC(C)(C)CC[C@]4(C(=O)O)CC[C@]23C)C1(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
NPO43806	Lantana	Genus	Verbenaceae	Eukaryota	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

Activity Type	# Activity
IC50	2
Apoptotic activity	1

Activity Type	# Activity
Cell line	1
Organism	1
Unchecked	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
NPT916	Cell line	SK-MEL	Homo sapiens	IC50	n.a.	n.a.	nM	PMID[10450948]
NPT28438	Unchecked	Unchecked	n.a.	Apoptotic activity	n.a.	n.a.	n.a.	PMID[10450948]
NPT605	Organism	Homo sapiens	Homo sapiens	IC50	n.a.	n.a.	nM	PMID[10450948]

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 NPC608622 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	21883
0.1-0.2	23884
0.2-0.3	3360
0.3-0.4	499
0.4-0.5	199
0.5-0.6	25
0.6-0.7	4
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
0.7612	Intermediate Similarity	NPC120840
0.6806	Remote Similarity	NPC74751
0.6471	Remote Similarity	NPC480944
0.6216	Remote Similarity	NPC481316
0.6133	Remote Similarity	NPC296164
0.5921	Remote Similarity	NPC488521
0.5714	Remote Similarity	NPC482712
0.5595	Remote Similarity	NPC283849
0.5479	Remote Similarity	NPC31031
0.5455	Remote Similarity	NPC485589
0.5455	Remote Similarity	NPC480949
0.5333	Remote Similarity	NPC30522
0.5325	Remote Similarity	NPC139570
0.525	Remote Similarity	NPC96580
0.5233	Remote Similarity	NPC606107
0.5195	Remote Similarity	NPC158141
0.5185	Remote Similarity	NPC485586
0.5185	Remote Similarity	NPC485588
0.5158	Remote Similarity	NPC610795
0.5128	Remote Similarity	NPC200752
0.5114	Remote Similarity	NPC286347
0.5111	Remote Similarity	NPC284807
0.5111	Remote Similarity	NPC473538
0.5065	Remote Similarity	NPC156981
0.5063	Remote Similarity	NPC610635
0.506	Remote Similarity	NPC481362
0.5057	Remote Similarity	NPC28198
0.5057	Remote Similarity	NPC476123
0.5056	Remote Similarity	NPC100383
0.5055	Remote Similarity	NPC191410

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC608622 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6128
0.1-0.2	2962
0.2-0.3	49
0.3-0.4	4
0.4-0.5	3
0.5-0.6	3
0.6-0.7	1
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
0.6806	Remote Similarity	NPD7748	Pre-clinical
0.5949	Remote Similarity	NPD7902	Phase 4
0.5244	Remote Similarity	NPD7900	Approved
0.5244	Remote Similarity	NPD7901	Clinical (unspecified phase)

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