NPASS Compound

Natural Product: NPC594

Natural Product ID	NPC594
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	Petroformynic Acid B
IUPAC Name	(4Z,20Z,26Z,30E,34S,43E,45S)-34,45-dihydroxyheptatetraconta-4,20,26,30,43-pentaen-2,32,35,46-tetraynoic acid
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL249074
PubChem CID	24179503
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0000262] Fatty acids and conjugates [CHEMONTID:0002950] Very long-chain fatty acids

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 2D 119118 0 0 0 0 0 0 0 0999 V2000 1.8481 -2.7990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5490 -2.0490 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.7500 3.8971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5000 5.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2500 6.4952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0000 7.7942 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7500 9.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5000 10.3923 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2500 11.6913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9510 12.4413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6519 13.1913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3529 13.9413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3529 15.4413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0538 16.1913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7548 16.9413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4558 17.6913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4558 19.1913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7548 19.9413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0538 20.6913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3529 21.4413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6519 22.1913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9510 22.9413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9510 24.4413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6519 25.1913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3529 25.9413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0538 26.6913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7548 27.4413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4558 28.1913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8433 28.9413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1423 29.6913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4413 30.4413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7404 31.1913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0394 31.9413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.3385 32.6913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6375 33.4413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.9365 34.1913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.2356 34.9413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.5346 35.6913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.8336 34.9413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.8336 33.4413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.8336 31.9413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.8336 30.4413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.5346 29.6913 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -15.1327 29.6913 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.5490 10.9413 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.0490 -0.5490 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.1471 -3.5490 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 -2.5981 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7500 1.2990 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2500 -1.2990 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5490 0.5490 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9510 2.0490 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7010 3.3481 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.2990 1.8481 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0490 3.1471 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4510 4.6471 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7990 4.4462 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2010 5.9462 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9510 7.2452 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5490 5.7452 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2990 7.0442 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7010 8.5442 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 9.0000 12.9904 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0538 13.1913 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6519 16.1913 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8038 17.4904 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3038 14.8923 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4860 17.9117 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0048 15.6423 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8433 16.9413 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8433 19.9413 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0048 21.2404 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4860 18.9710 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3038 21.9904 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8038 19.3923 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6029 22.7404 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1029 20.1423 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4019 20.8923 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9207 23.1617 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2500 22.1913 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 8.2500 25.1913 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4019 26.4904 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9207 24.2210 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1029 27.2404 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6029 24.6423 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3038 25.3923 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8038 27.9904 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5048 28.7404 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0048 26.1423 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2942 26.8923 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2058 29.4904 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0933 30.2404 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5933 27.6423 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8923 28.3923 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3923 30.9904 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1913 29.1423 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6913 31.7404 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9904 32.4904 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4904 29.8923 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7894 30.6423 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2894 33.2404 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.5885 33.9904 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0885 31.3923 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.3875 32.1423 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8875 34.7404 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1865 35.4904 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.6865 32.8923 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -11.9856 33.6423 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -10.4856 36.2404 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -12.5346 37.1913 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -15.1327 35.6913 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -15.1327 28.1913 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 10.8481 11.6913 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3481 -1.2990 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 3 0 2 3 1 0 3 4 1 0 4 5 2 0 5 6 1 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 3 0 13 14 1 0 14 15 1 0 15 16 3 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 2 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 27 28 2 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 1 0 32 33 1 0 33 34 1 0 34 35 1 0 35 36 1 0 36 37 1 0 37 38 1 0 38 39 1 0 39 40 1 0 40 41 1 0 41 42 1 0 42 43 1 0 43 44 2 0 44 45 1 0 45 46 3 0 46 47 1 0 47 48 2 0 47 49 1 0 14 50 1 0 3 51 1 0 1 52 1 0 3 53 1 6 4 54 1 0 5 55 1 0 6 56 1 0 6 57 1 0 7 58 1 0 7 59 1 0 8 60 1 0 8 61 1 0 9 62 1 0 9 63 1 0 10 64 1 0 10 65 1 0 11 66 1 0 11 67 1 0 14 68 1 6 17 69 1 0 18 70 1 0 19 71 1 0 19 72 1 0 20 73 1 0 20 74 1 0 21 75 1 0 22 76 1 0 23 77 1 0 23 78 1 0 24 79 1 0 24 80 1 0 25 81 1 0 25 82 1 0 26 83 1 0 26 84 1 0 27 85 1 0 28 86 1 0 29 87 1 0 29 88 1 0 30 89 1 0 30 90 1 0 31 91 1 0 31 92 1 0 32 93 1 0 32 94 1 0 33 95 1 0 33 96 1 0 34 97 1 0 34 98 1 0 35 99 1 0 35100 1 0 36101 1 0 36102 1 0 37103 1 0 37104 1 0 38105 1 0 38106 1 0 39107 1 0 39108 1 0 40109 1 0 40110 1 0 41111 1 0 41112 1 0 42113 1 0 42114 1 0 43115 1 0 44116 1 0 49117 1 0 50118 1 0 51119 1 0 M END

Standard InCHIKey	BZLCFINUEDERAD-JCPHLTBWSA-N
Standard InCHI	InChI=1S/C47H68O4/c1-2-45(48)41-37-33-29-27-28-31-35-39-43-46(49)42-38-34-30-25-23-21-19-17-15-13-11-9-7-5-3-4-6-8-10-12-14-16-18-20-22-24-26-32-36-40-44-47(50)51/h1,7,9,19,21,30,32,34,36-37,41,45-46,48-49H,3-6,8,10-18,20,22-29,31,33,35H2,(H,50,51)/b9-7-,21-19-,34-30+,36-32-,41-37+/t45-,46-/m1/s1
SMILES	C#C[C@H](/C=C/CCCCCCC#C[C@@H](C#C/C=C/CC/C=CCCCC/C=CCCCCCCCCCCCCCC/C=CC#CC(=O)O)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
NPO32455	pertrosia sp.	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[17985844]

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
IC50	1

Activity Type	# Activity
Cell line	1

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
NPT168	Cell line	P388	Mus musculus	IC50	=	0.4	ug.mL-1	PMID[19150154]

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 NPC594 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	38318
0.1-0.2	10976
0.2-0.3	458
0.3-0.4	53
0.4-0.5	26
0.5-0.6	12
0.6-0.7	8
0.7-0.8	0
0.8-0.85	0
0.85-0.9	1
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8519	High Similarity	NPC48968
0.7885	Intermediate Similarity	NPC470964
0.7647	Intermediate Similarity	NPC311648
0.7593	Intermediate Similarity	NPC474513
0.7255	Intermediate Similarity	NPC224148
0.72	Intermediate Similarity	NPC470963
0.7115	Intermediate Similarity	NPC329608
0.6897	Remote Similarity	NPC475984
0.6792	Remote Similarity	NPC146551
0.6364	Remote Similarity	NPC470965
0.6154	Remote Similarity	NPC89824
0.6154	Remote Similarity	NPC475477
0.6154	Remote Similarity	NPC256656
0.6154	Remote Similarity	NPC294278
0.6154	Remote Similarity	NPC477723
0.569	Remote Similarity	NPC152668
0.5614	Remote Similarity	NPC473896
0.5614	Remote Similarity	NPC473735
0.5593	Remote Similarity	NPC473652
0.5517	Remote Similarity	NPC473847
0.5517	Remote Similarity	NPC473721
0.5517	Remote Similarity	NPC473725
0.5517	Remote Similarity	NPC473910
0.5517	Remote Similarity	NPC475384
0.5517	Remote Similarity	NPC473532
0.537	Remote Similarity	NPC197272
0.5323	Remote Similarity	NPC168407

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC594 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	7352
0.1-0.2	1763
0.2-0.3	34
0.3-0.4	1
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