NPASS Compound

Natural Product: NPC483449

Natural Product ID	NPC483449
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	IBKUUFSNNUGZHT-SREVYHEPSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0001831] Carbonyl compounds [CHEMONTID:0000118] Ketones [CHEMONTID:0003670] Aryl ketones [CHEMONTID:0004296] Phenylketones [CHEMONTID:0004298] Alkyl-phenylketones

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 5.7528 0.0457 1.2770 C 0 0 0 0 0 0 0 0 0 0 0 0 5.9989 -0.6142 -0.0634 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4786 0.2633 -1.1777 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9777 0.5077 -1.0328 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2022 -0.7199 -1.0664 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4511 -1.0984 -0.0685 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3200 -0.3421 1.1538 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8342 0.0325 1.3043 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4311 0.8549 0.1165 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0046 1.3011 0.1309 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8995 0.1057 0.1546 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3419 0.4778 0.1632 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7786 1.7832 0.1504 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1359 2.0930 0.1590 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0603 1.0871 0.1805 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6288 -0.2242 0.1935 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2726 -0.5319 0.1849 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8727 -1.9329 0.1993 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6974 -2.4976 1.2968 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6858 -2.6452 -1.0679 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.5900 -1.2184 0.2152 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5687 3.4169 0.1459 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1138 -0.6054 1.8855 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2395 1.0295 1.1144 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6946 0.2949 1.8099 H 0 0 0 0 0 0 0 0 0 0 0 0 7.0999 -0.6869 -0.1787 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6033 -1.6312 -0.0921 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7115 -0.2128 -2.1522 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0212 1.2268 -1.1525 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7281 1.0462 -2.0109 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7588 1.2505 -0.2776 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2761 -1.3339 -1.9937 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8683 -2.0435 -0.1242 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8974 0.5462 1.3181 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4975 -1.0049 2.0623 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6680 0.6141 2.2275 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2219 -0.9139 1.3458 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1327 1.7312 0.0854 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6675 0.2532 -0.7890 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2247 1.9972 0.9573 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1754 1.8777 -0.8072 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7106 -0.4992 -0.7437 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7263 -0.4435 1.1054 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0447 2.5823 0.1333 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1089 1.3505 0.1869 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1582 -3.6435 -1.0005 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5961 -2.7899 -1.3068 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0854 -2.0464 -1.9207 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3005 -2.1599 0.0366 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9789 4.0706 -0.3505 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 2 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 16 21 1 0 14 22 1 0 17 12 1 0 1 23 1 0 1 24 1 0 1 25 1 0 2 26 1 0 2 27 1 0 3 28 1 0 3 29 1 0 4 30 1 0 4 31 1 0 5 32 1 0 6 33 1 0 7 34 1 0 7 35 1 0 8 36 1 0 8 37 1 0 9 38 1 0 9 39 1 0 10 40 1 0 10 41 1 0 11 42 1 0 11 43 1 0 13 44 1 0 15 45 1 0 20 46 1 0 20 47 1 0 20 48 1 0 21 49 1 0 22 50 1 0 M END

Standard InCHIKey	IBKUUFSNNUGZHT-SREVYHEPSA-N
Standard InCHI	InChI=1S/C19H28O3/c1-3-4-5-6-7-8-9-10-11-12-16-13-17(21)14-18(22)19(16)15(2)20/h6-7,13-14,21-22H,3-5,8-12H2,1-2H3/b7-6-
SMILES	CCCC/C=CCCCCCc1cc(cc(c1C(=O)C)O)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 NPC483449 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	19249
0.1-0.2	26620
0.2-0.3	3640
0.3-0.4	253
0.4-0.5	64
0.5-0.6	21
0.6-0.7	2
0.7-0.8	0
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.975	High Similarity	NPC483450
0.8049	Intermediate Similarity	NPC473691
0.8049	Intermediate Similarity	NPC477454
0.6667	Remote Similarity	NPC259942
0.6667	Remote Similarity	NPC92624
0.5778	Remote Similarity	NPC53051
0.5778	Remote Similarity	NPC24404
0.5778	Remote Similarity	NPC313030
0.5652	Remote Similarity	NPC146798
0.5652	Remote Similarity	NPC222522
0.5652	Remote Similarity	NPC106396
0.5652	Remote Similarity	NPC94351
0.5652	Remote Similarity	NPC168303
0.5333	Remote Similarity	NPC470700
0.5333	Remote Similarity	NPC54844
0.5333	Remote Similarity	NPC39097
0.5333	Remote Similarity	NPC302681
0.5333	Remote Similarity	NPC118286
0.5333	Remote Similarity	NPC109691
0.5306	Remote Similarity	NPC71002
0.5306	Remote Similarity	NPC302219
0.5306	Remote Similarity	NPC249828
0.5106	Remote Similarity	NPC39664
0.5102	Remote Similarity	NPC483454
0.5102	Remote Similarity	NPC162314
0.5102	Remote Similarity	NPC477453

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC483449 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4525
0.1-0.2	4487
0.2-0.3	134
0.3-0.4	3
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