NPASS Compound

Natural Product: NPC117691

Natural Product ID	NPC117691
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	PRAUVHZJPXOEIF-VGKQSNDQSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	6710742
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001553] Triterpenoids

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 84 88 0 0 0 0 0 0 0 0999 V2000 6.0185 -1.1917 2.2583 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4480 -0.4309 1.0421 C 0 0 2 0 0 0 0 0 0 0 0 0 5.4974 1.0123 1.3921 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3481 1.8079 0.8429 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7559 1.2246 -0.4249 C 0 0 2 0 0 0 0 0 0 0 0 0 2.8063 2.2428 -0.9736 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4554 1.7704 -1.3439 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8645 0.8847 -0.2959 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5108 1.7198 0.9109 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7989 -0.1713 0.1484 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2249 -1.1856 0.8353 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1967 -1.3013 1.1535 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0579 -0.3786 0.3926 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4769 -0.8664 0.1552 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.6143 -2.1256 -0.5854 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0050 -1.1012 1.5795 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.4771 -1.3187 1.6103 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1290 -0.0585 1.0875 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.7119 0.1765 -0.3496 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.3333 -0.8355 -1.2230 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3260 1.5327 -0.7109 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7807 2.4640 0.1687 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.2323 0.3241 -0.3938 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6761 0.8577 -1.6731 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2204 1.2241 -1.5169 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3984 0.1779 -0.8192 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.0549 -0.8722 -1.8220 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9244 0.1028 -2.7851 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4918 -0.1424 1.2455 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8435 -1.4352 2.9606 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2192 -0.1294 -0.1449 C 0 0 2 0 0 0 0 0 0 0 0 0 4.0734 -0.9529 0.7683 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2425 -2.3702 0.2562 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8346 1.1191 -1.4656 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9524 1.5674 -1.2422 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5204 0.5138 -2.6470 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1950 -1.4022 2.9550 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8119 -0.6126 2.7410 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4518 -2.1613 1.9471 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1620 -0.6718 0.2319 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5714 1.1487 2.5111 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4346 1.4481 1.0052 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6116 2.8707 0.6325 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5720 1.8222 1.6123 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2072 2.7667 -1.8975 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6940 3.1117 -0.2610 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8014 2.6904 -1.4076 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4777 1.3617 -2.3545 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3890 2.3359 0.8010 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5336 1.1147 1.8563 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3377 2.4670 1.0813 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9576 -1.9505 1.1375 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4672 -2.3748 1.0653 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3103 -1.0870 2.2552 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2384 0.5226 1.0608 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2864 -2.8617 -0.0467 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6673 -2.7164 -0.7146 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0554 -2.0579 -1.5997 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5095 -1.9934 2.0287 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7836 -0.1651 2.1312 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8354 -2.2173 1.1109 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7386 0.7824 1.6954 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4368 -0.5837 -1.2777 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0008 -0.8312 -2.2693 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3223 -1.8790 -0.8387 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1965 1.7610 -1.7662 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4213 1.4808 -0.4307 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1301 3.3743 0.0274 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0085 1.1419 0.3664 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1980 1.8457 -1.8541 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1407 2.2335 -1.0775 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8050 1.3126 -2.5588 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6042 -0.4506 -2.6393 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4118 -1.7510 -1.3821 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9963 -1.1303 -2.3866 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4727 0.4969 -3.5473 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8064 -1.0772 1.1162 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1490 -2.3619 3.1800 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3126 -0.6706 -1.1556 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6099 -1.0928 1.7918 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2444 -2.5246 -0.1968 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0332 -3.1395 1.0144 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5096 -2.5346 -0.5862 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1995 0.3542 -3.3792 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 1 8 10 1 0 10 11 2 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 6 14 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 24 25 1 0 25 26 1 0 26 27 1 6 24 28 1 0 18 29 1 0 17 30 1 0 10 31 1 0 31 32 1 0 32 33 1 0 5 34 1 6 34 35 2 0 34 36 1 0 32 2 1 0 31 5 1 0 26 8 1 0 26 13 1 0 23 14 1 0 1 37 1 0 1 38 1 0 1 39 1 0 2 40 1 6 3 41 1 0 3 42 1 0 4 43 1 0 4 44 1 0 6 45 1 0 6 46 1 0 7 47 1 0 7 48 1 0 9 49 1 0 9 50 1 0 9 51 1 0 11 52 1 0 12 53 1 0 12 54 1 0 13 55 1 0 15 56 1 0 15 57 1 0 15 58 1 0 16 59 1 0 16 60 1 0 17 61 1 6 18 62 1 1 20 63 1 0 20 64 1 0 20 65 1 0 21 66 1 0 21 67 1 0 22 68 1 0 23 69 1 0 24 70 1 6 25 71 1 0 25 72 1 0 27 73 1 0 27 74 1 0 27 75 1 0 28 76 1 0 29 77 1 0 30 78 1 0 31 79 1 6 32 80 1 1 33 81 1 0 33 82 1 0 33 83 1 0 36 84 1 0 M END

Standard InCHIKey	PRAUVHZJPXOEIF-VGKQSNDQSA-N
Standard InCHI	InChI=1S/C30H48O6/c1-16-9-10-30(25(35)36)12-11-28(5)18(22(30)17(16)2)7-8-21-26(3)13-20(33)24(34)27(4,15-31)23(26)19(32)14-29(21,28)6/h7,16-17,19-24,31-34H,8-15H2,1-6H3,(H,35,36)/t16-,17+,19-,20-,21?,22+,23?,24+,26-,27+,28-,29-,30+/m1/s1
SMILES	C[C@@H]1CC[C@@]2(CC[C@]3(C)C(=CCC4[C@@]5(C)C[C@H]([C@@H]([C@@](C)(CO)C5[C@@H](C[C@@]34C)O)O)O)[C@@H]2[C@H]1C)C(=O)O

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
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[ 17560738]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1007/s11816-015-0350-y]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	aerial part	n.a.	PMID[17520525]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22966846]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[MetaboLights]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO11144	Centella asiatica	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO11144	Centella asiatica	Species	Apiaceae	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

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 NPC117691 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	24370
0.1-0.2	22166
0.2-0.3	2797
0.3-0.4	344
0.4-0.5	103
0.5-0.6	45
0.6-0.7	16
0.7-0.8	0
0.8-0.85	3
0.85-0.9	0
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC305464
1.0	High Similarity	NPC19376
1.0	High Similarity	NPC25848
0.8125	Intermediate Similarity	NPC32407
0.8125	Intermediate Similarity	NPC263548
0.8125	Intermediate Similarity	NPC606320
0.7424	Intermediate Similarity	NPC71074
0.7424	Intermediate Similarity	NPC605937
0.7273	Intermediate Similarity	NPC307282
0.6812	Remote Similarity	NPC40092
0.6812	Remote Similarity	NPC87095
0.6667	Remote Similarity	NPC61543
0.6667	Remote Similarity	NPC293048
0.6667	Remote Similarity	NPC225585
0.6429	Remote Similarity	NPC37221
0.6301	Remote Similarity	NPC20235
0.6301	Remote Similarity	NPC299996
0.6301	Remote Similarity	NPC117663
0.6286	Remote Similarity	NPC51700
0.6286	Remote Similarity	NPC88716
0.6286	Remote Similarity	NPC68160
0.6232	Remote Similarity	NPC43686
0.6197	Remote Similarity	NPC88116
0.6111	Remote Similarity	NPC173089
0.6027	Remote Similarity	NPC247139
0.5972	Remote Similarity	NPC231063
0.5972	Remote Similarity	NPC282395
0.5972	Remote Similarity	NPC173744
0.5972	Remote Similarity	NPC204961
0.5972	Remote Similarity	NPC73004
0.5972	Remote Similarity	NPC609452
0.5946	Remote Similarity	NPC137072
0.5915	Remote Similarity	NPC477289
0.589	Remote Similarity	NPC477288
0.5844	Remote Similarity	NPC230151
0.5789	Remote Similarity	NPC479743
0.5775	Remote Similarity	NPC274050
0.5775	Remote Similarity	NPC162632
0.5753	Remote Similarity	NPC73489
0.5753	Remote Similarity	NPC130278
0.5753	Remote Similarity	NPC110308
0.5733	Remote Similarity	NPC25299
0.5733	Remote Similarity	NPC481322
0.5694	Remote Similarity	NPC274330
0.5541	Remote Similarity	NPC472149
0.5541	Remote Similarity	NPC300351
0.5526	Remote Similarity	NPC477290
0.5467	Remote Similarity	NPC259733
0.5467	Remote Similarity	NPC158371
0.5467	Remote Similarity	NPC207922
0.5405	Remote Similarity	NPC84319
0.5405	Remote Similarity	NPC52021
0.5405	Remote Similarity	NPC599947
0.5395	Remote Similarity	NPC118519
0.5395	Remote Similarity	NPC485589
0.5357	Remote Similarity	NPC57362
0.5342	Remote Similarity	NPC277399
0.5326	Remote Similarity	NPC479747
0.5326	Remote Similarity	NPC479746
0.5294	Remote Similarity	NPC177246
0.5256	Remote Similarity	NPC481318
0.52	Remote Similarity	NPC64872
0.52	Remote Similarity	NPC25906
0.5195	Remote Similarity	NPC201657
0.5132	Remote Similarity	NPC481314
0.5128	Remote Similarity	NPC127689
0.5125	Remote Similarity	NPC485586
0.5125	Remote Similarity	NPC485588
0.5065	Remote Similarity	NPC291028
0.5065	Remote Similarity	NPC145667

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC117691 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6566
0.1-0.2	2542
0.2-0.3	40
0.3-0.4	2
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