NPASS Compound

Natural Product: NPC469960

Natural Product ID	NPC469960
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Roridin L
IUPAC Name	n.a.
Synonyms	Roridin L
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL136268
PubChem CID	73355875
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids [CHEMONTID:0001789] Trichothecenes

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 76 80 0 0 0 0 0 0 0 0999 V2000 -3.6287 -1.7055 3.1728 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6355 -0.9602 1.8779 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2755 -1.6252 0.7573 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3180 -0.7974 -0.4566 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6275 0.5039 -0.1214 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6210 1.2764 0.7196 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0367 0.4548 1.9106 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2979 0.4810 0.4453 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1151 0.3552 1.8747 O 0 0 0 0 0 0 0 0 0 0 0 0 0.2575 0.4276 2.2249 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9864 0.6176 1.2419 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9104 0.3098 3.4745 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2414 0.3884 3.5950 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0991 0.6189 2.4310 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9046 -0.5852 1.9765 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3324 -0.2908 0.6242 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3063 -1.5277 -0.0452 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8893 -1.6302 -0.5732 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3136 -0.6509 -1.1660 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7552 0.6692 -1.5067 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0772 1.6312 -2.0590 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6661 1.6216 -2.4448 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2543 2.6100 -3.0861 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1948 0.6914 -2.1586 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4010 0.2782 -2.2188 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5035 1.1130 -1.5513 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7686 0.7060 -2.2600 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9784 1.2782 -2.3873 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0456 1.5124 -3.4734 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3810 -0.6802 -2.7549 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0873 -0.2172 -3.5013 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4796 -1.3379 -4.0173 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.0055 -1.3866 -1.6354 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2941 2.5652 -1.5088 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4010 -1.8736 -0.9003 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6714 -0.9797 -2.1045 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6061 -1.9139 -0.1210 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7922 0.2315 4.9476 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6828 -1.7354 3.5317 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2888 -2.7501 3.0499 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0548 -1.1693 3.9586 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9920 -2.6573 0.7900 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4253 -0.5101 -0.5592 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1898 2.2227 1.1013 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5234 1.4357 0.1087 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6198 0.8872 2.8615 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1482 0.4864 2.0595 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6282 -0.3380 0.0466 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7985 1.4807 0.2438 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3388 0.1591 4.3336 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9964 1.3144 2.8267 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7737 1.2212 1.6075 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3258 -1.4970 1.9511 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8238 -0.7220 2.5568 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2672 -2.3085 0.8187 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3819 -2.5559 -0.4418 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2850 -0.8386 -1.4873 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7623 0.8829 -1.2617 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5914 2.5536 -2.2682 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4500 -0.7916 -1.6520 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8855 0.6723 -2.6729 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2831 2.2581 -1.9851 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0875 -1.1418 -3.4234 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2989 0.5811 -4.2046 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7718 -2.1221 -3.4902 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1828 3.0644 -1.0171 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3621 2.8811 -1.0424 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3299 2.9586 -2.5451 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3536 -2.9326 -1.2895 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5471 -1.3714 -2.6789 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9256 0.0139 -1.6984 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7753 -0.9826 -2.7432 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3138 -1.3946 -0.5678 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2681 -0.5805 5.5218 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6367 1.1718 5.5470 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8674 -0.0252 4.8924 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 5 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 10 12 1 0 12 13 2 3 13 14 1 0 14 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 2 3 19 20 1 0 20 21 2 3 21 22 1 0 22 23 2 0 22 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 1 0 28 29 1 0 27 30 1 0 30 31 1 0 31 32 1 0 30 33 1 0 26 34 1 0 17 35 1 0 35 36 1 0 35 37 1 0 13 38 1 0 7 2 1 0 33 4 1 0 26 5 1 0 31 25 1 0 29 27 1 0 1 39 1 0 1 40 1 0 1 41 1 0 3 42 1 0 4 43 1 0 6 44 1 0 6 45 1 0 7 46 1 0 7 47 1 0 8 48 1 0 8 49 1 0 12 50 1 0 14 51 1 0 14 52 1 0 15 53 1 0 15 54 1 0 17 55 1 0 18 56 1 0 19 57 1 0 20 58 1 0 21 59 1 0 25 60 1 0 28 61 1 0 28 62 1 0 30 63 1 0 31 64 1 0 32 65 1 0 34 66 1 0 34 67 1 0 34 68 1 0 35 69 1 0 36 70 1 0 36 71 1 0 36 72 1 0 37 73 1 0 38 74 1 0 38 75 1 0 38 76 1 0 M END

Standard InCHIKey	CXUYRNDRKDXIHC-PWSVTAGBSA-N
Standard InCHI	InChI=1S/C29H38O9/c1-17-9-11-28-15-35-23(32)14-18(2)10-12-34-20(19(3)30)7-5-6-8-22(31)38-25-24(33)26(37-21(28)13-17)29(16-36-29)27(25,28)4/h5-8,13-14,19-21,24-26,30,33H,9-12,15-16H2,1-4H3/b7-5+,8-6-,18-14+/t19-,20+,21+,24+,25+,26+,27+,28+,29-/m0/s1
SMILES	CC1=CC2C3(CC1)COC(=O)C=C(CCOC(C=CC=CC(=O)OC4C3(C5(CO5)C(C4O)O2)C)C(C)O)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
NPO30443	Myrothecium verrucaria	Species	Stachybotryaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10075777]
NPO30443	Myrothecium verrucaria	Species	Stachybotryaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[13678412]
NPO30443	Myrothecium verrucaria	Species	Stachybotryaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21539317]
NPO30443	Myrothecium verrucaria	Species	Stachybotryaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO30443	Myrothecium verrucaria	Species	Stachybotryaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

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
Concentration	1
Selectivity	5
IC50	17

Activity Type	# Activity
Cell line	21
Non-molecular	2

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
NPT730	Cell line	MC-38	Mus musculus	Selectivity	=	-400.0	zone unit	PMID[13678412]
NPT730	Cell line	MC-38	Mus musculus	Selectivity	=	0.0	zone unit	PMID[13678412]
NPT137	Cell line	L1210	Mus musculus	Selectivity	=	400.0	zone unit	PMID[13678412]
NPT404	Cell line	CCRF-CEM	Homo sapiens	IC50	>	10000.0	nM	PMID[7561907]
NPT116	Cell line	HL-60	Homo sapiens	IC50	>	10000.0	nM	PMID[18163584]
NPT112	Cell line	MOLT-4	Homo sapiens	IC50	>	10000.0	nM	PMID[18163584]
NPT81	Cell line	A549	Homo sapiens	IC50	>	10000.0	nM	PMID[20028081]
NPT405	Cell line	NCI-H226	Homo sapiens	IC50	=	91.0	nM	PMID[20028081]
NPT455	Cell line	NCI-H522	Homo sapiens	IC50	=	21.0	nM	PMID[17512736]
NPT407	Cell line	COLO 205	Homo sapiens	IC50	=	13.0	nM	PMID[15270556]
NPT393	Cell line	HCT-116	Homo sapiens	IC50	>	10000.0	nM	PubChem BioAssay data set
NPT148	Cell line	HCT-15	Homo sapiens	IC50	>	10000.0	nM	PMID[18341287]
NPT387	Cell line	M14	Homo sapiens	IC50	=	24.0	nM	PMID[23398362]
NPT147	Cell line	SK-MEL-2	Homo sapiens	IC50	=	24.0	nM	PMID[18341287]
NPT398	Cell line	UACC-62	Homo sapiens	IC50	=	18.0	nM	PubChem BioAssay data set
NPT376	Cell line	A498	Homo sapiens	IC50	=	19.0	nM	PubChem BioAssay data set
NPT406	Cell line	RXF 393	Homo sapiens	IC50	>	10000.0	nM	PMID[21428459]
NPT83	Cell line	MCF7	Homo sapiens	IC50	>	10000.0	nM	PMID[18341287]
NPT400	Cell line	MDA-MB-435	Homo sapiens	IC50	=	20.0	nM	PMID[18341287]
NPT367	Cell line	MDA-N	Homo sapiens	IC50	=	21.0	nM	PMID[21051535]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	Concentration	=	1.3	ug ml-1	PMID[13678412]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	Selectivity	=	-100.0	zone unit	PMID[13678412]
NPT22117	Cell line	NCI-H125	Homo sapiens	Selectivity	=	-50.0	zone unit	PMID[13678412]

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 NPC469960 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	20732
0.1-0.2	28000
0.2-0.3	1056
0.3-0.4	14
0.4-0.5	28
0.5-0.6	15
0.6-0.7	9
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC93026
0.8529	High Similarity	NPC265502
0.75	Intermediate Similarity	NPC29389
0.75	Intermediate Similarity	NPC112316
0.6875	Remote Similarity	NPC287075
0.675	Remote Similarity	NPC108682
0.6707	Remote Similarity	NPC484149
0.6625	Remote Similarity	NPC484920
0.6582	Remote Similarity	NPC65700
0.6377	Remote Similarity	NPC240838
0.6377	Remote Similarity	NPC600295
0.6322	Remote Similarity	NPC484153
0.6322	Remote Similarity	NPC484925
0.593	Remote Similarity	NPC101965
0.593	Remote Similarity	NPC101400
0.5904	Remote Similarity	NPC13743
0.5897	Remote Similarity	NPC98813
0.5897	Remote Similarity	NPC600365
0.5753	Remote Similarity	NPC605097
0.5517	Remote Similarity	NPC484924
0.5488	Remote Similarity	NPC484152
0.5479	Remote Similarity	NPC79631
0.5111	Remote Similarity	NPC484923
0.5111	Remote Similarity	NPC484922
0.5057	Remote Similarity	NPC469959
0.5057	Remote Similarity	NPC469957
0.5057	Remote Similarity	NPC98038
0.5057	Remote Similarity	NPC313921

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC469960 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7236
0.1-0.2	1905
0.2-0.3	9
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