NPASS Compound

Natural Product: NPC73489

Natural Product ID	NPC73489
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	AWZFLHHIQVOKDV-JHHOYTOVSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
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 4.8555 0.9686 -2.0987 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0166 0.6118 -0.6324 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4051 1.1918 -0.2891 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1573 -0.8571 -0.4718 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9386 -1.6028 0.0082 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4968 -0.9099 1.2816 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4681 -1.6468 2.0881 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1177 -1.0170 2.0966 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6422 -0.7414 0.7391 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4770 -2.0997 0.0581 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6803 0.1100 0.0433 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3067 0.5484 -1.1406 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0149 0.2786 -1.8040 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0649 -0.0986 -0.8218 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.4520 0.3765 -1.1339 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.4933 1.7909 -1.5345 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8465 -0.3792 -2.4234 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2619 -0.0540 -2.8210 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2601 -0.3618 -1.7464 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.8635 0.1676 -0.3842 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.3927 1.5211 -0.1028 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6423 -0.7636 0.5817 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2901 -2.0770 0.4356 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4310 -0.1086 -0.1121 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.0329 0.0499 1.3234 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.6486 -0.4279 1.5817 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6244 0.0797 0.5915 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3212 1.4968 0.9944 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3365 1.2629 1.9010 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4866 0.2045 -2.0898 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9273 0.3968 0.7642 C 0 0 2 0 0 0 0 0 0 0 0 0 3.9303 1.2734 0.1482 C 0 0 2 0 0 0 0 0 0 0 0 0 3.3518 2.3690 -0.4892 O 0 0 0 0 0 0 0 0 0 0 0 0 4.7046 -0.6931 2.1129 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9880 0.4136 2.5678 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5290 -1.7731 2.3784 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3501 1.9552 -2.1363 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1358 0.2573 -2.5955 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8195 0.9950 -2.6353 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0452 1.1766 -1.1769 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8494 0.6747 0.5825 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2166 2.2416 0.0143 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4109 -1.3030 -1.4789 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0032 -1.1506 0.1826 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2579 -2.6392 0.2157 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1494 -1.5210 -0.7385 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8083 -1.5863 3.1801 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5385 -2.7064 1.8717 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4200 -1.7738 2.5652 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1252 -0.1708 2.7992 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5008 -2.5650 0.3624 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6771 -2.0968 -1.0082 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2093 -2.8581 0.4689 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0536 1.1448 -1.6609 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2838 1.1950 -2.3981 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1745 -0.4861 -2.6039 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1474 -1.2358 -0.9483 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5453 2.1916 -1.6639 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1229 1.8668 -2.5959 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8868 2.5002 -0.9633 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7848 -1.4701 -2.2494 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1801 -0.0802 -3.2360 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4957 -0.7127 -3.6865 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3753 0.9811 -3.2079 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4108 -1.4606 -1.7153 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7387 2.2462 0.3696 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3153 1.5315 0.5616 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8349 1.9060 -1.0738 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6529 -0.3627 1.6005 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7131 -0.6600 0.2269 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4264 -2.5352 1.3076 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3693 -1.2487 -0.2464 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6903 -0.6857 1.8951 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6134 -1.5317 1.7130 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3216 -0.0240 2.5847 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1337 2.1285 0.2388 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2623 1.4548 1.9480 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2486 2.0600 1.3060 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6914 1.1974 2.8201 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9982 -0.3948 -2.7029 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5839 0.9002 1.7281 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4914 1.8107 0.9910 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9402 3.1587 -0.5195 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1617 -1.8147 3.1804 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 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 6 9 11 1 0 11 12 2 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 6 15 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 6 20 22 1 0 22 23 1 0 20 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 1 25 29 1 0 19 30 1 0 11 31 1 0 31 32 1 0 32 33 1 0 6 34 1 1 34 35 2 0 34 36 1 0 32 2 1 0 31 6 1 0 27 9 1 0 27 14 1 0 24 15 1 0 1 37 1 0 1 38 1 0 1 39 1 0 3 40 1 0 3 41 1 0 3 42 1 0 4 43 1 0 4 44 1 0 5 45 1 0 5 46 1 0 7 47 1 0 7 48 1 0 8 49 1 0 8 50 1 0 10 51 1 0 10 52 1 0 10 53 1 0 12 54 1 0 13 55 1 0 13 56 1 0 14 57 1 1 16 58 1 0 16 59 1 0 16 60 1 0 17 61 1 0 17 62 1 0 18 63 1 0 18 64 1 0 19 65 1 1 21 66 1 0 21 67 1 0 21 68 1 0 22 69 1 0 22 70 1 0 23 71 1 0 24 72 1 6 25 73 1 1 26 74 1 0 26 75 1 0 28 76 1 0 28 77 1 0 28 78 1 0 29 79 1 0 30 80 1 0 31 81 1 1 32 82 1 1 33 83 1 0 36 84 1 0 M END

Standard InCHIKey	AWZFLHHIQVOKDV-JHHOYTOVSA-N
Standard InCHI	InChI=1S/C30H48O6/c1-25(2)11-13-30(24(35)36)14-12-28(5)17(21(30)23(25)34)7-8-19-26(3)10-9-20(33)27(4,16-31)22(26)18(32)15-29(19,28)6/h7,18-23,31-34H,8-16H2,1-6H3,(H,35,36)/t18-,19-,20+,21-,22-,23+,26-,27-,28-,29-,30+/m1/s1
SMILES	CC1(C)CC[C@@]2(CC[C@]3(C)C(=CC[C@@H]4[C@@]5(C)CC[C@@H]([C@@](C)(CO)[C@@H]5[C@@H](C[C@@]34C)O)O)[C@@H]2[C@@H]1O)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
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[16309325]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	Seoul, Korea	2000-Jun	PMID[16643034]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruit	n.a.	n.a.	PMID[18505286]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruit	n.a.	n.a.	PMID[19650637]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[23305920]
NPO13017	Nauclea latifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31429278]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[32141747]
NPO1654	Schefflera arboricola	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO11953	Lolium temulentum	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO1654	Schefflera arboricola	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO1654	Schefflera arboricola	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO1654	Schefflera arboricola	Species	Araliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11953	Lolium temulentum	Species	Poaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9518	Gardenia jasminoides	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13017	Nauclea latifolia	Species	Rubiaceae	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
MIC	1
MBC	1
Ratio	1
EC50	1

Activity Type	# Activity
Organism	3
Cell line	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
NPT1122	Organism	Haemophilus influenzae	Haemophilus influenzae	MIC	=	18.8	ug.mL-1	PMID[31429278]
NPT1122	Organism	Haemophilus influenzae	Haemophilus influenzae	MBC	=	50.0	ug ml-1	PMID[31429278]
NPT1122	Organism	Haemophilus influenzae	Haemophilus influenzae	Ratio	=	2.7	n.a.	PMID[31429278]
NPT27675	Cell line	NRK-52E	Rattus norvegicus	EC50	=	117.5	nM	PMID[32141747]

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 NPC73489 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	24273
0.1-0.2	22289
0.2-0.3	2691
0.3-0.4	445
0.4-0.5	106
0.5-0.6	39
0.6-0.7	8
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
0.7656	Intermediate Similarity	NPC229281
0.7619	Intermediate Similarity	NPC43686
0.7538	Intermediate Similarity	NPC130278
0.7206	Intermediate Similarity	NPC137072
0.697	Remote Similarity	NPC187722
0.6618	Remote Similarity	NPC64872
0.6618	Remote Similarity	NPC25906
0.6522	Remote Similarity	NPC173744
0.6522	Remote Similarity	NPC204961
0.6522	Remote Similarity	NPC73004
0.6338	Remote Similarity	NPC118519
0.6056	Remote Similarity	NPC111214
0.5915	Remote Similarity	NPC307282
0.5833	Remote Similarity	NPC38754
0.5753	Remote Similarity	NPC305464
0.5753	Remote Similarity	NPC19376
0.5753	Remote Similarity	NPC25848
0.5694	Remote Similarity	NPC270768
0.5694	Remote Similarity	NPC59263
0.5694	Remote Similarity	NPC210106
0.5694	Remote Similarity	NPC121798
0.5694	Remote Similarity	NPC234346
0.5676	Remote Similarity	NPC191412
0.5676	Remote Similarity	NPC114159
0.5676	Remote Similarity	NPC6818
0.5616	Remote Similarity	NPC61543
0.5616	Remote Similarity	NPC293048
0.5616	Remote Similarity	NPC225585
0.5526	Remote Similarity	NPC116457
0.5479	Remote Similarity	NPC194196
0.5479	Remote Similarity	NPC290972
0.5395	Remote Similarity	NPC127689
0.5395	Remote Similarity	NPC130520
0.5333	Remote Similarity	NPC291028
0.5333	Remote Similarity	NPC136697
0.527	Remote Similarity	NPC182797
0.527	Remote Similarity	NPC52169
0.527	Remote Similarity	NPC488562
0.5135	Remote Similarity	NPC480946
0.5135	Remote Similarity	NPC130577
0.5135	Remote Similarity	NPC142415
0.5135	Remote Similarity	NPC102683
0.5132	Remote Similarity	NPC202728
0.5132	Remote Similarity	NPC158059
0.5132	Remote Similarity	NPC476318
0.5067	Remote Similarity	NPC51700
0.5067	Remote Similarity	NPC88716
0.5067	Remote Similarity	NPC68160
0.5065	Remote Similarity	NPC476327
0.5065	Remote Similarity	NPC263393
0.5062	Remote Similarity	NPC327179

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC73489 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6720
0.1-0.2	2390
0.2-0.3	35
0.3-0.4	5
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