NPASS Compound

Natural Product: NPC608258

Natural Product ID	NPC608258
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	LYLDPYNWDVVPIQ-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL124885
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 44 46 0 0 0 0 0 0 0 0999 V2000 7.5539 -0.1460 -0.2007 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5567 -0.3472 0.7868 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2195 -0.2737 0.4242 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8212 -0.0107 -0.8685 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4580 0.0533 -1.1844 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5003 -0.1377 -0.2472 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0620 -0.0952 -0.4575 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5733 0.1603 -1.7137 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7920 0.2131 -1.9747 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2890 0.4419 -3.0996 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6396 -0.0047 -0.9057 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0067 0.0196 -1.0264 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5570 0.2751 -2.2829 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8463 1.6141 -2.6974 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8415 -0.2023 0.0629 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2265 -0.1634 -0.1301 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.8394 -1.3989 -0.4705 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3066 -0.4545 1.3027 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1064 -0.6780 2.3998 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5545 -0.9395 3.6847 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9485 -0.4756 1.4078 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0997 -0.2576 0.3379 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1953 -0.2895 0.4960 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9629 -0.4021 1.0527 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2697 -0.4732 1.4033 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6158 -0.7420 2.7242 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6463 0.9265 -0.4563 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3454 -0.6920 -1.1382 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5254 -0.5455 0.1784 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5552 0.1492 -1.6529 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1699 0.2607 -2.2034 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2222 0.3327 -2.5598 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7398 1.6036 -3.8104 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8945 1.8963 -2.4658 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1188 2.3310 -2.2729 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1180 -2.0922 -0.9400 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.6136 -1.1811 -1.2263 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2568 -1.8717 0.4522 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7758 -1.7320 3.5927 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0562 0.0047 4.0136 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3247 -1.1996 4.4204 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5089 -0.6760 2.3933 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2193 -0.5590 1.8222 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9884 -1.6330 3.0295 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 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 13 14 1 0 12 15 1 0 15 16 1 0 16 17 1 0 15 18 2 0 18 19 1 0 19 20 1 0 18 21 1 0 21 22 2 0 22 23 1 0 6 24 1 0 24 25 2 0 25 26 1 0 25 3 1 0 23 7 1 0 22 11 1 0 1 27 1 0 1 28 1 0 1 29 1 0 4 30 1 0 5 31 1 0 8 32 1 0 14 33 1 0 14 34 1 0 14 35 1 0 17 36 1 0 17 37 1 0 17 38 1 0 20 39 1 0 20 40 1 0 20 41 1 0 21 42 1 0 24 43 1 0 26 44 1 0 M END

Standard InCHIKey	LYLDPYNWDVVPIQ-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C19H18O7/c1-22-13-6-5-10(7-11(13)20)14-8-12(21)17-15(26-14)9-16(23-2)18(24-3)19(17)25-4/h5-9,20H,1-4H3
SMILES	COc1ccc(-c2cc(=O)c3c(OC)c(OC)c(OC)cc3o2)cc1O

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
NPO22900	Orthosiphon stamineus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11374950]
NPO22900	Orthosiphon stamineus	Species	Lamiaceae	Eukaryota	n.a.	Indonesia	n.a.	PMID[12467611]
NPO22900	Orthosiphon stamineus	Species	Lamiaceae	Eukaryota	aerial parts	Bangdung, Indonesia	2000-Aug	PMID[12608860]
NPO22900	Orthosiphon stamineus	Species	Lamiaceae	Eukaryota	n.a.	Taiwan	n.a.	PMID[15104497]
NPO22900	Orthosiphon stamineus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO22900	Orthosiphon stamineus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO22900	Orthosiphon stamineus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO22900	Orthosiphon stamineus	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO22900	Orthosiphon stamineus	Species	Lamiaceae	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
Activity	6
Ki	2
TIME	2
IC50	2
Ratio IC50	1

Activity Type	# Activity
Individual protein	6
Cell line	7

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1603	Individual protein	Cytochrome P450 1A1	Homo sapiens	Activity	=	20.4	%	PMID[21482471]
NPT1604	Individual protein	Cytochrome P450 1B1	Homo sapiens	Ki	=	670.0	nM	PMID[21482471]
NPT1603	Individual protein	Cytochrome P450 1A1	Homo sapiens	TIME	=	0.1483	hr	PMID[21482471]
NPT1603	Individual protein	Cytochrome P450 1A1	Homo sapiens	Ki	=	630.0	nM	PMID[21482471]
NPT781	Individual protein	Tubulin alpha chain	Sus scrofa	IC50	>	50000.0	nM	PMID[14552774]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT139	Cell line	HT-29	Homo sapiens	Activity	=	95.4	n.a.	PMID[15828817]
NPT139	Cell line	HT-29	Homo sapiens	Activity	=	102.1	n.a.	PMID[15828817]
NPT2257	Cell line	MCF-10A	Homo sapiens	Activity	n.a.	n.a.	n.a.	PMID[21482471]
NPT784	Cell line	MDA-MB-468	Homo sapiens	Ratio IC50	=	100.0	n.a.	PMID[21482471]
NPT111	Cell line	K562	Homo sapiens	IC50	=	22000.0	nM	PMID[14552774]
NPT784	Cell line	MDA-MB-468	Homo sapiens	Activity	n.a.	n.a.	n.a.	PMID[21482471]
NPT30063	Cell line	Monocyte	Homo sapiens	Activity	=	0.0	n.a.	PMID[8882428]

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 NPC608258 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	27675
0.1-0.2	18670
0.2-0.3	2722
0.3-0.4	575
0.4-0.5	164
0.5-0.6	29
0.6-0.7	9
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
0.7778	Intermediate Similarity	NPC604569
0.7368	Intermediate Similarity	NPC606105
0.7358	Intermediate Similarity	NPC14958
0.7193	Intermediate Similarity	NPC75215
0.7143	Intermediate Similarity	NPC50715
0.7091	Intermediate Similarity	NPC215932
0.6897	Remote Similarity	NPC160951
0.6852	Remote Similarity	NPC106461
0.6667	Remote Similarity	NPC302408
0.661	Remote Similarity	NPC287101
0.6552	Remote Similarity	NPC256283
0.6441	Remote Similarity	NPC212678
0.6333	Remote Similarity	NPC223579
0.6066	Remote Similarity	NPC52005
0.6066	Remote Similarity	NPC607642
0.5862	Remote Similarity	NPC600022
0.5833	Remote Similarity	NPC22519
0.5806	Remote Similarity	NPC196439
0.5645	Remote Similarity	NPC292460
0.5645	Remote Similarity	NPC146165
0.5556	Remote Similarity	NPC25495
0.5484	Remote Similarity	NPC603827
0.5424	Remote Similarity	NPC69752
0.541	Remote Similarity	NPC138360
0.541	Remote Similarity	NPC609062
0.5397	Remote Similarity	NPC605582
0.5323	Remote Similarity	NPC145379
0.5312	Remote Similarity	NPC93376
0.5246	Remote Similarity	NPC23955
0.5246	Remote Similarity	NPC259058
0.5238	Remote Similarity	NPC9609
0.5238	Remote Similarity	NPC25270
0.5167	Remote Similarity	NPC101294
0.5161	Remote Similarity	NPC156222
0.5156	Remote Similarity	NPC300943
0.5156	Remote Similarity	NPC69394
0.5156	Remote Similarity	NPC167815
0.5156	Remote Similarity	NPC270620
0.5156	Remote Similarity	NPC20830
0.5156	Remote Similarity	NPC255350
0.5079	Remote Similarity	NPC100887
0.5079	Remote Similarity	NPC70853
0.5079	Remote Similarity	NPC57030
0.5077	Remote Similarity	NPC283600

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC608258 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5072
0.1-0.2	3980
0.2-0.3	91
0.3-0.4	3
0.4-0.5	3
0.5-0.6	1
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
0.5156	Remote Similarity	NPD2801	Pre-clinical

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