NPASS Compound

Natural Product: NPC483454

Natural Product ID	NPC483454
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	OTYINVFQXIKPBE-WAYWQWQTSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	118045944
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0002448] Benzenoids [CHEMONTID:0000134] Phenols [CHEMONTID:0004647] 1-hydroxy-4-unsubstituted benzenoids

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 50 50 0 0 0 0 0 0 0 0999 V2000 7.5288 0.4886 -1.0206 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9889 0.5868 0.3643 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4265 0.4662 0.3551 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0900 -0.8293 -0.2181 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7775 -1.3594 -0.3784 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6022 -0.9211 -0.0800 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3461 0.3597 0.5597 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6585 0.2697 1.8956 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3475 -0.4179 1.7891 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6587 0.2463 0.8872 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9377 -0.5840 0.9366 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9927 0.0332 0.0475 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2277 -0.8685 0.1666 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3057 -0.3100 -0.6904 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4329 -0.6903 -2.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4418 -0.1581 -2.7767 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3548 0.7616 -2.2927 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2079 1.1314 -0.9680 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2092 0.6129 -0.1770 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.1310 2.0634 -0.4728 O 0 0 0 0 0 0 0 0 0 0 0 0 8.4788 1.0986 -1.0479 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8356 0.7648 -1.8138 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8895 -0.5718 -1.1641 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2004 1.5495 0.8717 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3088 -0.2335 1.0307 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1911 0.6004 1.4238 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1760 1.3278 -0.3021 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5185 -0.7757 -1.2868 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8365 -1.6067 0.1953 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7542 -2.3861 -0.8739 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7405 -1.5964 -0.3458 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0945 1.1389 0.5038 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5252 0.8256 -0.0911 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3027 -0.0883 2.7068 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4287 1.3437 2.1772 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1193 -0.5299 2.8021 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4374 -1.4688 1.3933 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3150 0.2629 -0.1893 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8419 1.2874 1.2202 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2560 -0.6421 1.9763 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7214 -1.5898 0.5560 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6544 0.0749 -1.0066 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2316 1.0304 0.4397 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5488 -0.8972 1.2123 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9034 -1.8727 -0.1829 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7248 -1.4130 -2.4009 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5461 -0.4593 -3.8218 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1424 1.1711 -2.9149 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1038 0.9029 0.8404 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4752 1.8714 0.4745 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 17 18 1 0 18 19 2 0 18 20 1 0 19 14 1 0 1 21 1 0 1 22 1 0 1 23 1 0 2 24 1 0 2 25 1 0 3 26 1 0 3 27 1 0 4 28 1 0 4 29 1 0 5 30 1 0 6 31 1 0 7 32 1 0 7 33 1 0 8 34 1 0 8 35 1 0 9 36 1 0 9 37 1 0 10 38 1 0 10 39 1 0 11 40 1 0 11 41 1 0 12 42 1 0 12 43 1 0 13 44 1 0 13 45 1 0 15 46 1 0 16 47 1 0 17 48 1 0 19 49 1 0 20 50 1 0 M END

Standard InCHIKey	OTYINVFQXIKPBE-WAYWQWQTSA-N
Standard InCHI	InChI=1S/C19H30O/c1-2-3-4-5-6-7-8-9-10-11-12-14-18-15-13-16-19(20)17-18/h5-6,13,15-17,20H,2-4,7-12,14H2,1H3/b6-5-
SMILES	CCCC/C=CCCCCCCCc1cccc(c1)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
NPO40175	Knema hookeriana	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27008174]
NPO40175	Knema hookeriana	Species	Myristicaceae	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
Ki	2

Activity Type	# Activity
Protein-protein interaction	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
NPT21617	Protein-protein interaction	Induced myeloid leukemia cell differentiation protein Mcl-1/BH3-interacting domain death agonist	Homo sapiens	Ki	>	33000.0	nM	PMID[27008174]
NPT21616	Protein-protein interaction	Bcl-xL/BAK	Homo sapiens	Ki	>	23000.0	nM	PMID[27008174]

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 NPC483454 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	24413
0.1-0.2	22321
0.2-0.3	2785
0.3-0.4	195
0.4-0.5	65
0.5-0.6	36
0.6-0.7	18
0.7-0.8	0
0.8-0.85	4
0.85-0.9	2
0.9-0.95	0
0.95-1	3

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC162314
0.9722	High Similarity	NPC94139
0.9722	High Similarity	NPC147284
0.8974	High Similarity	NPC210497
0.8649	High Similarity	NPC487734
0.8056	Intermediate Similarity	NPC3358
0.8056	Intermediate Similarity	NPC306884
0.8056	Intermediate Similarity	NPC603092
0.8049	Intermediate Similarity	NPC192
0.75	Intermediate Similarity	NPC487735
0.7179	Intermediate Similarity	NPC53051
0.7179	Intermediate Similarity	NPC24404
0.7179	Intermediate Similarity	NPC313030
0.7105	Intermediate Similarity	NPC76938
0.7105	Intermediate Similarity	NPC32714
0.7	Intermediate Similarity	NPC146798
0.7	Intermediate Similarity	NPC222522
0.7	Intermediate Similarity	NPC106396
0.7	Intermediate Similarity	NPC94351
0.7	Intermediate Similarity	NPC168303
0.6944	Remote Similarity	NPC610566
0.6667	Remote Similarity	NPC470700
0.6667	Remote Similarity	NPC54844
0.6667	Remote Similarity	NPC39097
0.6667	Remote Similarity	NPC302681
0.6667	Remote Similarity	NPC118286
0.6667	Remote Similarity	NPC109691
0.6512	Remote Similarity	NPC71002
0.6512	Remote Similarity	NPC302219
0.6512	Remote Similarity	NPC249828
0.6429	Remote Similarity	NPC196479
0.6341	Remote Similarity	NPC39664
0.619	Remote Similarity	NPC55561
0.6136	Remote Similarity	NPC129373
0.6136	Remote Similarity	NPC242342
0.6136	Remote Similarity	NPC85479
0.6047	Remote Similarity	NPC487736
0.6047	Remote Similarity	NPC232523
0.5952	Remote Similarity	NPC177420
0.5946	Remote Similarity	NPC606762
0.5909	Remote Similarity	NPC488413
0.5909	Remote Similarity	NPC488412
0.5778	Remote Similarity	NPC10588
0.5745	Remote Similarity	NPC48730
0.5745	Remote Similarity	NPC294741
0.5652	Remote Similarity	NPC158253
0.5652	Remote Similarity	NPC72947
0.56	Remote Similarity	NPC305603
0.5556	Remote Similarity	NPC166761
0.55	Remote Similarity	NPC294186
0.55	Remote Similarity	NPC147310
0.55	Remote Similarity	NPC137415
0.55	Remote Similarity	NPC166313
0.55	Remote Similarity	NPC123273
0.55	Remote Similarity	NPC192032
0.55	Remote Similarity	NPC318325
0.55	Remote Similarity	NPC24407
0.55	Remote Similarity	NPC11280
0.5476	Remote Similarity	NPC241891
0.5476	Remote Similarity	NPC134829
0.5455	Remote Similarity	NPC280347
0.5435	Remote Similarity	NPC284011
0.5417	Remote Similarity	NPC219070
0.5306	Remote Similarity	NPC483450
0.5294	Remote Similarity	NPC61033
0.5294	Remote Similarity	NPC249836
0.5278	Remote Similarity	NPC27974
0.5238	Remote Similarity	NPC25493
0.5208	Remote Similarity	NPC470161
0.5128	Remote Similarity	NPC246056
0.5116	Remote Similarity	NPC113460
0.5106	Remote Similarity	NPC488416
0.5102	Remote Similarity	NPC483449
0.5098	Remote Similarity	NPC248396

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC483454 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4797
0.1-0.2	4080
0.2-0.3	255
0.3-0.4	17
0.4-0.5	1
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