NPASS Compound

Natural Product: NPC472188

Natural Product ID	NPC472188
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	XDGNGAAYVBELLQ-PJJSSYIVSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL3343971
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001551] Diterpenoids [CHEMONTID:0001757] Colensane and clerodane diterpenoids

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 80 82 0 0 0 0 0 0 0 0999 V2000 -3.8764 -2.3886 -3.2837 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7684 -3.5099 -2.6165 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4855 -3.5982 -1.2110 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4264 -4.8306 -0.6720 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2734 -2.3994 -0.3495 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9999 -1.6703 -0.6349 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8151 -0.4434 0.2700 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7903 -0.9800 1.6586 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0193 0.4634 0.1828 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.3700 0.9224 -1.1850 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7855 1.5621 1.1645 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6067 2.4442 0.8081 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.4677 1.7259 0.1790 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6495 0.3229 -0.2199 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6445 -0.5082 -0.1458 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2952 -0.4286 1.2073 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5613 -1.0938 1.0606 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9719 -2.0956 1.8964 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1916 -2.4409 2.8355 O 0 0 0 0 0 0 0 0 0 0 0 0 4.2901 -2.7800 1.7348 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3730 -1.7414 1.8658 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7475 -2.3098 1.7212 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3106 -3.3669 0.3250 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6584 1.0333 1.3308 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8452 1.9667 0.8547 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9825 3.4618 0.7366 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5103 3.7023 -0.5293 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1278 2.6252 -1.0658 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6131 1.8932 -2.0122 O 0 0 0 0 0 0 0 0 0 0 0 0 0.1494 1.6857 -3.2823 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9611 2.1623 -3.5995 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8947 0.9160 -4.3281 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3444 3.8223 0.8268 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5304 4.6626 1.9223 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1841 3.4315 0.0040 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2601 4.6363 0.6579 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7580 -1.4374 -2.8062 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0919 -2.4180 -4.3518 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9034 -4.4574 -3.1687 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5781 -5.7132 -1.2379 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2131 -4.8764 0.3830 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1295 -1.7129 -0.6246 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3877 -2.7112 0.6881 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7580 -1.4766 -1.6765 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1946 -2.3787 -0.2368 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4227 -0.3481 2.4506 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8681 -1.1952 1.9349 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2947 -1.9804 1.7489 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8978 -0.1256 0.6048 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3924 0.5187 -1.4511 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5281 2.0343 -1.2705 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7134 0.5513 -1.9742 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7425 2.1574 1.2086 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6777 1.1352 2.1666 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2991 2.9400 1.7289 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8057 0.3420 -1.3524 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3529 0.0431 -0.8356 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5298 -1.4833 -0.5783 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8070 -0.8618 2.0396 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3937 -3.6103 2.4355 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2541 -1.2959 2.8919 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1651 -0.9206 1.1611 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7621 -3.4162 1.6439 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2038 -1.8793 0.8004 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3887 -1.9607 2.5818 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7968 -2.6630 -0.3852 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7970 -4.3456 0.3639 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3500 -3.5238 -0.0091 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5708 1.3605 1.7997 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4281 3.9330 1.5460 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0563 2.9500 -1.5361 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3938 -0.0466 -4.5512 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9479 0.7619 -4.0402 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8655 1.5449 -5.2522 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8982 5.5581 1.7552 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5834 4.9348 1.9908 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2316 4.1149 2.8480 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8485 4.5705 1.6113 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8635 5.3587 -0.0022 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3425 5.1743 0.8500 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 0 3 5 1 0 5 6 1 0 7 6 1 6 7 8 1 0 7 9 1 0 9 10 1 0 9 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 2 0 18 20 1 0 20 21 1 0 21 22 1 0 20 23 1 0 16 24 1 0 24 25 2 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 29 30 1 0 30 31 2 0 30 32 1 0 26 33 1 0 33 34 1 0 12 35 1 0 35 36 1 0 14 7 1 0 28 13 1 0 13 25 1 1 1 37 1 0 1 38 1 0 2 39 1 0 4 40 1 0 4 41 1 0 5 42 1 0 5 43 1 0 6 44 1 0 6 45 1 0 8 46 1 0 8 47 1 0 8 48 1 0 9 49 1 1 10 50 1 0 10 51 1 0 10 52 1 0 11 53 1 0 11 54 1 0 12 55 1 1 14 56 1 6 15 57 1 0 15 58 1 0 16 59 1 1 20 60 1 0 21 61 1 0 21 62 1 0 22 63 1 0 22 64 1 0 22 65 1 0 23 66 1 0 23 67 1 0 23 68 1 0 24 69 1 0 26 70 1 1 28 71 1 6 32 72 1 0 32 73 1 0 32 74 1 0 34 75 1 0 34 76 1 0 34 77 1 0 36 78 1 0 36 79 1 0 36 80 1 0 M END

Standard InCHIKey	XDGNGAAYVBELLQ-PJJSSYIVSA-N
Standard InCHI	InChI=1S/C29H44O7/c1-10-17(3)12-13-28(7)19(5)14-24(32-8)29-22(26(33-9)36-27(29)34-20(6)30)15-21(16-23(28)29)35-25(31)18(4)11-2/h10,15,18-19,21,23-24,26-27H,1,3,11-14,16H2,2,4-9H3/t18?,19-,21+,23+,24+,26+,27-,28-,29-/m1/s1
SMILES	C=CC(=C)CC[C@]1(C)[C@H](C)C[C@@H]([C@@]23[C@H]1C[C@@H](OC(=O)C(CC)C)C=C3[C@H](O[C@H]2OC(=O)C)OC)OC

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
NPO32459	casearia balansae	Species	Salicaceae	Eukaryota	leaves and twigs	n.a.	n.a.	PMID[24033131]
NPO32459	casearia balansae	Species	Salicaceae	Eukaryota	twigs	n.a.	n.a.	PMID[25286284]
NPO32459	casearia balansae	Species	Salicaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[26699618]
NPO32459	casearia balansae	Species	Salicaceae	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
EC50	1

Activity Type	# Activity
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
NPT681	Cell line	PC-12	Rattus norvegicus	EC50	=	4.0	ug.mL-1	PMID[25286284]

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 NPC472188 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	21952
0.1-0.2	25804
0.2-0.3	1963
0.3-0.4	34
0.4-0.5	42
0.5-0.6	27
0.6-0.7	15
0.7-0.8	0
0.8-0.85	7
0.85-0.9	5
0.9-0.95	3
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.9474	High Similarity	NPC471366
0.9474	High Similarity	NPC476800
0.9474	High Similarity	NPC488237
0.8929	High Similarity	NPC472189
0.8852	High Similarity	NPC472187
0.8772	High Similarity	NPC481018
0.8644	High Similarity	NPC488236
0.8621	High Similarity	NPC481020
0.8448	Intermediate Similarity	NPC171598
0.8226	Intermediate Similarity	NPC473545
0.8167	Intermediate Similarity	NPC471362
0.8167	Intermediate Similarity	NPC471372
0.8167	Intermediate Similarity	NPC318917
0.8167	Intermediate Similarity	NPC481019
0.8033	Intermediate Similarity	NPC472186
0.7903	Intermediate Similarity	NPC488649
0.7778	Intermediate Similarity	NPC481017
0.7344	Intermediate Similarity	NPC473204
0.6769	Remote Similarity	NPC488235
0.6618	Remote Similarity	NPC238397
0.6615	Remote Similarity	NPC488651
0.6615	Remote Similarity	NPC488648
0.6538	Remote Similarity	NPC488962
0.6522	Remote Similarity	NPC488963
0.6462	Remote Similarity	NPC606965
0.6418	Remote Similarity	NPC479937
0.6364	Remote Similarity	NPC132395
0.6364	Remote Similarity	NPC471364
0.6364	Remote Similarity	NPC600724
0.6143	Remote Similarity	NPC475889
0.6143	Remote Similarity	NPC7613
0.6143	Remote Similarity	NPC479942
0.6	Remote Similarity	NPC471365
0.5972	Remote Similarity	NPC471363
0.5909	Remote Similarity	NPC603601
0.5833	Remote Similarity	NPC48548
0.5811	Remote Similarity	NPC127933
0.5797	Remote Similarity	NPC479939
0.5758	Remote Similarity	NPC488650
0.5758	Remote Similarity	NPC481022
0.5652	Remote Similarity	NPC479934
0.5641	Remote Similarity	NPC473216
0.5571	Remote Similarity	NPC479935
0.5571	Remote Similarity	NPC479936
0.5493	Remote Similarity	NPC479943
0.5467	Remote Similarity	NPC125423
0.5395	Remote Similarity	NPC40728
0.5342	Remote Similarity	NPC479940
0.5342	Remote Similarity	NPC7644
0.5333	Remote Similarity	NPC488219
0.527	Remote Similarity	NPC88013
0.5263	Remote Similarity	NPC488221
0.5263	Remote Similarity	NPC488220
0.5263	Remote Similarity	NPC488216
0.525	Remote Similarity	NPC473399
0.5205	Remote Similarity	NPC479938
0.5067	Remote Similarity	NPC217921
0.5067	Remote Similarity	NPC135015
0.5067	Remote Similarity	NPC488658
0.5067	Remote Similarity	NPC488655

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC472188 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7208
0.1-0.2	1925
0.2-0.3	17
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