NPASS Compound

Natural Product: NPC601586

Natural Product ID	NPC601586
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	HQNSTFQMUGDYSO-XMHBHJPISA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL4860709
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 56 59 0 0 0 0 0 0 0 0999 V2000 9.3235 -0.5011 1.2624 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9998 -0.5937 1.7185 O 0 0 0 0 0 0 0 0 0 0 0 0 6.8889 -0.3820 0.9458 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9936 -0.0475 -0.3968 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8364 0.1587 -1.1438 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0091 0.4880 -2.4703 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5977 0.0295 -0.5465 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4816 0.2423 -1.3220 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5478 0.5444 -2.5324 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2391 0.0995 -0.6692 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1303 0.3149 -1.4556 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1507 -0.2294 0.6498 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8851 -0.3915 1.3811 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9653 -0.7338 2.7370 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1476 -0.9116 3.5215 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3631 -0.7459 2.9473 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5183 -0.9172 3.7090 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5222 -0.4065 1.6085 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7825 -0.2524 1.0835 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1816 0.0802 -0.2040 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.9523 1.2379 -0.1024 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0419 1.2864 -0.9266 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.7814 2.5902 -0.5911 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9158 2.7204 -1.3897 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0434 0.1775 -0.6699 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.7663 -0.0333 -1.8362 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.3504 -1.1104 -0.2949 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.3315 -1.2414 1.1005 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.9578 -1.0468 -0.8639 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.0610 -0.8178 -2.2332 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3561 -0.2380 0.8574 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2949 -0.4120 1.3030 O 0 0 0 0 0 0 0 0 0 0 0 0 4.4753 -0.3052 0.7979 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6388 -0.5027 1.5099 C 0 0 0 0 0 0 0 0 0 0 0 0 9.6366 0.5421 1.2001 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3819 -0.9725 0.2454 H 0 0 0 0 0 0 0 0 0 0 0 0 10.0405 -1.0435 1.9099 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9727 0.0432 -0.8221 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0762 1.4443 -2.8225 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0067 1.1067 -2.0797 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9645 -0.8634 3.1843 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0200 -1.1807 4.5831 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8428 -0.1917 4.3479 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2928 0.2320 -0.8421 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7963 1.3823 -2.0136 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0708 2.5099 0.4705 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1352 3.4697 -0.7335 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6885 2.2638 -0.9926 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7585 0.4373 0.1374 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2935 -0.8840 -1.7012 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9311 -1.9354 -0.7092 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1724 -0.9506 1.5087 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3919 -1.9978 -0.6688 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1729 -0.8210 -2.6651 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4798 0.0233 -0.1736 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5825 -0.7638 2.5540 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 1 0 5 7 2 0 7 8 1 0 8 9 2 0 8 10 1 0 10 11 1 0 10 12 2 0 12 13 1 0 13 14 2 0 14 15 1 0 15 16 2 0 16 17 1 0 16 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 22 25 1 0 25 26 1 0 25 27 1 0 27 28 1 0 27 29 1 0 29 30 1 0 18 31 2 0 12 32 1 0 32 33 1 0 33 34 2 0 34 3 1 0 33 7 1 0 31 13 1 0 29 20 1 0 1 35 1 0 1 36 1 0 1 37 1 0 4 38 1 0 6 39 1 0 11 40 1 0 14 41 1 0 15 42 1 0 17 43 1 0 20 44 1 6 22 45 1 6 23 46 1 0 23 47 1 0 24 48 1 0 25 49 1 1 26 50 1 0 27 51 1 6 28 52 1 0 29 53 1 6 30 54 1 0 31 55 1 0 34 56 1 0 M END

Standard InCHIKey	HQNSTFQMUGDYSO-XMHBHJPISA-N
Standard InCHI	InChI=1S/C22H22O12/c1-31-9-5-11(25)15-13(6-9)32-21(19(29)17(15)27)8-2-3-10(24)12(4-8)33-22-20(30)18(28)16(26)14(7-23)34-22/h2-6,14,16,18,20,22-26,28-30H,7H2,1H3/t14-,16-,18+,20-,22-/m1/s1
SMILES	COc1cc(O)c2c(=O)c(O)c(-c3ccc(O)c(O[C@@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4O)c3)oc2c1

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
NPO50019	Eucalyptus rostrata	Genus	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO46560	Peltophorum pterocarpum	Species	Fabaceae	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
Activity	2
FC	2

Activity Type	# Activity
Cell line	2
Unchecked	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
NPT4727	Cell line	C3H 10T1/2	Mus musculus	FC	=	1.3	n.a.	PMID[34407463]
NPT28438	Unchecked	Unchecked	n.a.	Activity	=	17.0	%	PMID[34407463]

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 NPC601586 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	23067
0.1-0.2	22584
0.2-0.3	2846
0.3-0.4	905
0.4-0.5	296
0.5-0.6	109
0.6-0.7	32
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8182	Intermediate Similarity	NPC486578
0.7949	Intermediate Similarity	NPC197285
0.7895	Intermediate Similarity	NPC277205
0.7895	Intermediate Similarity	NPC37919
0.7895	Intermediate Similarity	NPC323593
0.7895	Intermediate Similarity	NPC203500
0.7821	Intermediate Similarity	NPC285197
0.75	Intermediate Similarity	NPC601144
0.7407	Intermediate Similarity	NPC311830
0.716	Intermediate Similarity	NPC307938
0.6806	Remote Similarity	NPC252933
0.6707	Remote Similarity	NPC245014
0.6707	Remote Similarity	NPC84265
0.6667	Remote Similarity	NPC108831
0.6667	Remote Similarity	NPC238376
0.6667	Remote Similarity	NPC182634
0.6627	Remote Similarity	NPC117260
0.6512	Remote Similarity	NPC469931
0.6506	Remote Similarity	NPC84362
0.6429	Remote Similarity	NPC21100
0.6395	Remote Similarity	NPC607707
0.6279	Remote Similarity	NPC22832
0.6279	Remote Similarity	NPC243930
0.6279	Remote Similarity	NPC601710
0.6265	Remote Similarity	NPC39360
0.6265	Remote Similarity	NPC29763
0.6265	Remote Similarity	NPC210003
0.6222	Remote Similarity	NPC275454
0.6207	Remote Similarity	NPC602805
0.619	Remote Similarity	NPC297987
0.619	Remote Similarity	NPC95090
0.619	Remote Similarity	NPC27408
0.619	Remote Similarity	NPC136042
0.619	Remote Similarity	NPC189142
0.619	Remote Similarity	NPC77660
0.6146	Remote Similarity	NPC135358
0.6136	Remote Similarity	NPC203050
0.6136	Remote Similarity	NPC488072
0.6136	Remote Similarity	NPC225434
0.6092	Remote Similarity	NPC101026
0.6092	Remote Similarity	NPC488077
0.6	Remote Similarity	NPC282987
0.59	Remote Similarity	NPC480796
0.5882	Remote Similarity	NPC289667
0.587	Remote Similarity	NPC67105
0.5843	Remote Similarity	NPC206123
0.5843	Remote Similarity	NPC116458
0.5843	Remote Similarity	NPC246943
0.5843	Remote Similarity	NPC605784
0.5824	Remote Similarity	NPC251417
0.5814	Remote Similarity	NPC609879
0.5773	Remote Similarity	NPC195257
0.5747	Remote Similarity	NPC22195
0.5747	Remote Similarity	NPC21190
0.5698	Remote Similarity	NPC261866
0.5698	Remote Similarity	NPC254306
0.5612	Remote Similarity	NPC80068
0.56	Remote Similarity	NPC87125
0.56	Remote Similarity	NPC143799
0.5579	Remote Similarity	NPC131745
0.5568	Remote Similarity	NPC46420
0.5568	Remote Similarity	NPC271692
0.5568	Remote Similarity	NPC73511
0.5517	Remote Similarity	NPC476405
0.5474	Remote Similarity	NPC183672
0.5455	Remote Similarity	NPC93337
0.5455	Remote Similarity	NPC200740
0.5455	Remote Similarity	NPC146792
0.5455	Remote Similarity	NPC166753
0.5443	Remote Similarity	NPC227192
0.5422	Remote Similarity	NPC191154
0.5393	Remote Similarity	NPC58716
0.5393	Remote Similarity	NPC24043
0.5393	Remote Similarity	NPC105025
0.5393	Remote Similarity	NPC488080
0.5393	Remote Similarity	NPC45638
0.5393	Remote Similarity	NPC169977
0.5393	Remote Similarity	NPC603655
0.5393	Remote Similarity	NPC610763
0.5385	Remote Similarity	NPC284960
0.5385	Remote Similarity	NPC605067
0.5385	Remote Similarity	NPC609478
0.5368	Remote Similarity	NPC227508
0.5361	Remote Similarity	NPC64425
0.5341	Remote Similarity	NPC58053
0.5333	Remote Similarity	NPC42773
0.5333	Remote Similarity	NPC45522
0.5333	Remote Similarity	NPC325555
0.5333	Remote Similarity	NPC226304
0.5333	Remote Similarity	NPC201292
0.5321	Remote Similarity	NPC470720
0.5316	Remote Similarity	NPC125062
0.5281	Remote Similarity	NPC197896
0.5281	Remote Similarity	NPC313163
0.5275	Remote Similarity	NPC488071
0.5275	Remote Similarity	NPC609451
0.5275	Remote Similarity	NPC611303
0.5269	Remote Similarity	NPC479407
0.5263	Remote Similarity	NPC152042
0.5258	Remote Similarity	NPC169733
0.525	Remote Similarity	NPC473045
0.5229	Remote Similarity	NPC470719
0.5229	Remote Similarity	NPC470717
0.5227	Remote Similarity	NPC331652
0.5222	Remote Similarity	NPC304745
0.5222	Remote Similarity	NPC186807
0.5217	Remote Similarity	NPC120099
0.5217	Remote Similarity	NPC21666
0.5213	Remote Similarity	NPC4390
0.5213	Remote Similarity	NPC477848
0.5189	Remote Similarity	NPC277532
0.5185	Remote Similarity	NPC295625
0.5176	Remote Similarity	NPC134819
0.5169	Remote Similarity	NPC249281
0.5169	Remote Similarity	NPC77672
0.5169	Remote Similarity	NPC45618
0.5169	Remote Similarity	NPC133671
0.5169	Remote Similarity	NPC19709
0.5169	Remote Similarity	NPC135391
0.5169	Remote Similarity	NPC78263
0.5169	Remote Similarity	NPC250069
0.5165	Remote Similarity	NPC222936
0.5165	Remote Similarity	NPC472459
0.5165	Remote Similarity	NPC27942
0.5165	Remote Similarity	NPC599850
0.5161	Remote Similarity	NPC223747
0.5161	Remote Similarity	NPC88023
0.5161	Remote Similarity	NPC136761
0.5161	Remote Similarity	NPC309025
0.5158	Remote Similarity	NPC8856
0.5143	Remote Similarity	NPC219043
0.5125	Remote Similarity	NPC137062
0.5125	Remote Similarity	NPC78326
0.5111	Remote Similarity	NPC145038
0.5111	Remote Similarity	NPC56077
0.5111	Remote Similarity	NPC281131
0.5111	Remote Similarity	NPC168822
0.5111	Remote Similarity	NPC253662
0.5111	Remote Similarity	NPC179950
0.5111	Remote Similarity	NPC158674
0.5111	Remote Similarity	NPC88789
0.5111	Remote Similarity	NPC234739
0.5111	Remote Similarity	NPC491374
0.5109	Remote Similarity	NPC191306
0.5109	Remote Similarity	NPC60735
0.5109	Remote Similarity	NPC26230
0.5109	Remote Similarity	NPC80140
0.5106	Remote Similarity	NPC48773
0.51	Remote Similarity	NPC35119
0.5055	Remote Similarity	NPC181712
0.5051	Remote Similarity	NPC240306

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC601586 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5645
0.1-0.2	3422
0.2-0.3	66
0.3-0.4	11
0.4-0.5	6
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