NPASS Compound

Natural Product: NPC610677

Natural Product ID	NPC610677
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	VJRBXZFHKYDEQV-KPHYXMJDSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL2087144
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 79 82 0 0 0 0 0 0 0 0999 V2000 8.6793 -0.5238 0.7520 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5517 -0.1174 -0.1741 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5644 1.3893 -0.2774 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6867 -0.7047 -1.4293 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2614 -0.5217 0.5016 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0556 -0.1447 -0.3737 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7723 -0.5735 0.3516 C 0 0 1 0 0 0 0 0 0 0 0 0 3.8349 0.1600 1.5606 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5495 -0.1592 -0.4554 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5141 -0.9576 -1.7361 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6940 1.1849 -0.7426 O 0 0 0 0 0 0 0 0 0 0 0 0 1.2821 -0.4453 0.3185 C 0 0 1 0 0 0 0 0 0 0 0 0 1.3064 0.3434 1.6419 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1435 0.7288 1.9194 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8857 -0.0944 0.9561 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.9886 -1.3896 1.4038 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2313 0.3810 0.5736 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7979 1.4558 1.0318 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1305 1.8278 0.5811 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8653 2.6531 1.1792 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.6526 1.1940 -0.6607 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.1148 1.4489 -0.8633 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9796 0.6428 0.0458 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.9610 -0.0362 -0.6973 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2700 -0.2439 1.0027 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.2019 -1.2345 1.4034 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0669 -0.9473 0.5146 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.3888 -2.2656 0.1414 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3177 -0.2599 -0.6162 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.7761 -0.9769 -1.8853 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8841 -0.5301 -0.4198 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0261 -0.4311 -1.6580 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5872 -0.7852 -1.3663 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0210 0.0107 -0.2857 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0317 1.4659 -0.7021 C 0 0 0 0 0 0 0 0 0 0 0 0 8.9218 -1.5952 0.6896 H 0 0 0 0 0 0 0 0 0 0 0 0 9.5542 0.1073 0.5011 H 0 0 0 0 0 0 0 0 0 0 0 0 8.3691 -0.2378 1.7914 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8941 1.8623 0.4790 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5769 1.8159 -0.0776 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2068 1.7193 -1.2599 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4000 -1.6315 -1.4453 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2987 -1.6106 0.6740 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2261 -0.0157 1.4702 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2137 -0.7273 -1.3001 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0939 0.9400 -0.4992 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7270 -1.6497 0.5004 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2639 -0.3960 2.2827 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2999 -0.3350 -2.6296 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8068 -1.8358 -1.6439 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4916 -1.4819 -1.9517 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1740 1.6891 -0.0512 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2459 -1.5354 0.4957 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8402 1.3036 1.5241 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7255 -0.2862 2.4444 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3040 1.8282 1.8443 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3565 0.4869 2.9945 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7114 -2.0760 0.7670 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3077 2.0870 1.7434 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1224 1.6601 -1.5308 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3858 1.2418 -1.9228 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2620 2.5607 -0.7489 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.5803 1.3875 0.6505 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.7747 -0.1553 -0.1443 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0931 0.3318 1.9576 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0449 -0.8241 1.7073 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3748 -1.0733 1.3998 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0770 -2.6427 0.7326 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1622 -1.9003 -2.0522 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8187 -1.3469 -1.7991 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6469 -0.2949 -2.7320 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7905 -1.5628 0.0071 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0341 0.6182 -2.0162 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3569 -1.0667 -2.4880 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0530 -0.5347 -2.3322 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5457 -1.8739 -1.2656 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5896 2.1034 0.0012 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3708 1.5887 -1.7626 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0236 1.8146 -0.6886 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 2 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 7 9 1 0 9 10 1 0 9 11 1 6 9 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 1 15 17 1 0 17 18 2 0 18 19 1 0 19 20 2 0 19 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 23 25 1 0 25 26 1 0 25 27 1 0 27 28 1 0 27 29 1 0 29 30 1 6 29 31 1 0 31 32 1 0 32 33 1 0 33 34 1 0 34 35 1 6 34 12 1 0 34 15 1 0 31 17 1 0 29 21 1 0 1 36 1 0 1 37 1 0 1 38 1 0 3 39 1 0 3 40 1 0 3 41 1 0 4 42 1 0 5 43 1 0 5 44 1 0 6 45 1 0 6 46 1 0 7 47 1 1 8 48 1 0 10 49 1 0 10 50 1 0 10 51 1 0 11 52 1 0 12 53 1 1 13 54 1 0 13 55 1 0 14 56 1 0 14 57 1 0 16 58 1 0 18 59 1 0 21 60 1 6 22 61 1 0 22 62 1 0 23 63 1 1 24 64 1 0 25 65 1 1 26 66 1 0 27 67 1 1 28 68 1 0 30 69 1 0 30 70 1 0 30 71 1 0 31 72 1 1 32 73 1 0 32 74 1 0 33 75 1 0 33 76 1 0 35 77 1 0 35 78 1 0 35 79 1 0 M END

Standard InCHIKey	VJRBXZFHKYDEQV-KPHYXMJDSA-N
Standard InCHI	InChI=1S/C27H44O8/c1-23(2,33)9-8-20(30)26(5,34)19-7-11-27(35)15-12-17(28)16-13-18(29)21(31)22(32)25(16,4)14(15)6-10-24(19,27)3/h12,14,16,18-22,29-35H,6-11,13H2,1-5H3/t14-,16-,18+,19-,20+,21+,22+,24+,25+,26+,27+/m0/s1
SMILES	CC(C)(O)CC[C@@H](O)[C@](C)(O)[C@H]1CC[C@@]2(O)C3=CC(=O)[C@@H]4C[C@@H](O)[C@@H](O)[C@@H](O)[C@]4(C)[C@H]3CC[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
NPO223	Rhaponticum carthamoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15730237]
NPO223	Rhaponticum carthamoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO50633	Lychnis chalcedonica	Species	Caryophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO223	Rhaponticum carthamoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO223	Rhaponticum carthamoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO223	Rhaponticum carthamoides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO223	Rhaponticum carthamoides	Species	Asteraceae	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
FICI	3
Ratio	1

Activity Type	# Activity
Individual protein	4

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	FICI	=	2.42	n.a.	PMID[22578055]
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	FICI	=	1.31	n.a.	PMID[22578055]
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	Ratio	=	0.94	n.a.	PMID[22578055]
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	FICI	=	0.8	n.a.	PMID[22578055]

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 NPC610677 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	17451
0.1-0.2	29335
0.2-0.3	3010
0.3-0.4	11
0.4-0.5	15
0.5-0.6	11
0.6-0.7	17
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
0.7541	Intermediate Similarity	NPC50692
0.7541	Intermediate Similarity	NPC260268
0.7541	Intermediate Similarity	NPC152695
0.7541	Intermediate Similarity	NPC319077
0.7541	Intermediate Similarity	NPC97202
0.7541	Intermediate Similarity	NPC601752
0.7097	Intermediate Similarity	NPC600374
0.6719	Remote Similarity	NPC48733
0.6719	Remote Similarity	NPC171137
0.6667	Remote Similarity	NPC477916
0.6418	Remote Similarity	NPC202167
0.6418	Remote Similarity	NPC49958
0.6364	Remote Similarity	NPC296945
0.6364	Remote Similarity	NPC220229
0.6364	Remote Similarity	NPC601682
0.6212	Remote Similarity	NPC214264
0.6212	Remote Similarity	NPC475060
0.6212	Remote Similarity	NPC85829
0.6212	Remote Similarity	NPC83744
0.6154	Remote Similarity	NPC108721
0.6154	Remote Similarity	NPC73300
0.6143	Remote Similarity	NPC250109
0.6061	Remote Similarity	NPC11710
0.6056	Remote Similarity	NPC600136
0.589	Remote Similarity	NPC603170
0.5857	Remote Similarity	NPC476027
0.5694	Remote Similarity	NPC49492
0.5694	Remote Similarity	NPC266728
0.5588	Remote Similarity	NPC302607
0.5441	Remote Similarity	NPC150531
0.5362	Remote Similarity	NPC217201
0.5362	Remote Similarity	NPC451956
0.5342	Remote Similarity	NPC207251
0.5205	Remote Similarity	NPC317210
0.5065	Remote Similarity	NPC109973

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC610677 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6477
0.1-0.2	2542
0.2-0.3	131
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