NPASS Compound

Natural Product: NPC487734

Natural Product ID	NPC487734
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ACGPFWZDANXQSU-SNAWJCMRSA-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: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 38 38 0 0 0 0 0 0 0 0999 V2000 5.2281 -0.8086 -2.5496 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1518 -0.5203 -1.5551 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1065 -1.6086 -1.5631 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0180 -1.3879 -0.6078 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9612 -0.3442 0.1768 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8688 -0.0834 1.1635 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1701 1.2238 0.8495 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4677 1.2400 -0.5102 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5530 0.2464 -0.7063 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7301 0.3827 0.1377 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.7763 1.1987 -0.2559 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9170 1.3363 0.5342 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9965 0.6472 1.7220 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9807 -0.1597 2.1279 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8558 -0.2789 1.3216 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0698 -0.8504 3.3268 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2014 -0.9800 -2.0621 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9949 -1.7272 -3.1310 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3575 0.0333 -3.2602 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7512 0.4788 -1.6903 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6141 -0.5451 -0.5346 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5776 -2.6090 -1.4831 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6549 -1.5890 -2.5995 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2265 -2.1254 -0.5523 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7501 0.3871 0.1189 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1489 -0.9194 1.1658 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3163 0.0113 2.1742 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5826 1.4906 1.5897 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9851 2.0025 0.8493 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7742 2.2884 -0.7070 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3665 1.0032 -1.2358 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1119 -0.7696 -0.4716 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8056 0.1730 -1.8021 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6640 1.7167 -1.1956 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7196 1.9829 0.1986 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8887 0.7549 2.3402 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0988 -0.9382 1.7061 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4575 -0.3528 4.1417 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 2 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 9 10 1 0 10 11 2 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 14 16 1 0 15 10 1 0 1 17 1 0 1 18 1 0 1 19 1 0 2 20 1 0 2 21 1 0 3 22 1 0 3 23 1 0 4 24 1 0 5 25 1 0 6 26 1 0 6 27 1 0 7 28 1 0 7 29 1 0 8 30 1 0 8 31 1 0 9 32 1 0 9 33 1 0 11 34 1 0 12 35 1 0 13 36 1 0 15 37 1 0 16 38 1 0 M END

Standard InCHIKey	ACGPFWZDANXQSU-SNAWJCMRSA-N
Standard InCHI	InChI=1S/C15H22O/c1-2-3-4-5-6-7-8-10-14-11-9-12-15(16)13-14/h4-5,9,11-13,16H,2-3,6-8,10H2,1H3/b5-4+
SMILES	CCC/C=C/CCCCc1cccc(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
NPO40726	Hormoscilla sp. VPG 16-59	Strain	Gomontiellaceae	Bacteria	n.a.	n.a.	n.a.	PMID[30489078]
NPO40726	Hormoscilla sp. VPG 16-59	Strain	Gomontiellaceae	Bacteria	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
IC50	3
MIC	8

Activity Type	# Activity
Cell line	3
Organism	8

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
NPT82	Cell line	MDA-MB-231	Homo sapiens	IC50	=	27000.0	nM	PMID[30489078]
NPT81	Cell line	A549	Homo sapiens	IC50	=	37000.0	nM	PMID[30489078]
NPT393	Cell line	HCT-116	Homo sapiens	IC50	=	26000.0	nM	PMID[30489078]
NPT312	Organism	Saccharomyces cerevisiae	Saccharomyces cerevisiae	MIC	>	22.0	ug.mL-1	PMID[30489078]
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	MIC	>	22.0	ug.mL-1	PMID[30489078]
NPT18	Organism	Pseudomonas aeruginosa	Pseudomonas aeruginosa	MIC	>	22.0	ug.mL-1	PMID[30489078]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	22.0	ug.mL-1	PMID[30489078]
NPT16	Organism	Staphylococcus aureus	Staphylococcus aureus	MIC	=	16.0	ug.mL-1	PMID[32453590]
NPT314	Organism	Bacillus cereus	Bacillus cereus	MIC	=	11.0	ug.mL-1	PMID[30489078]
NPT314	Organism	Bacillus cereus	Bacillus cereus	MIC	=	16.0	ug.mL-1	PMID[32453590]

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 NPC487734 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	24652
0.1-0.2	22241
0.2-0.3	2663
0.3-0.4	179
0.4-0.5	73
0.5-0.6	30
0.6-0.7	8
0.7-0.8	0
0.8-0.85	4
0.85-0.9	2
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8649	High Similarity	NPC483454
0.8649	High Similarity	NPC162314
0.8421	Intermediate Similarity	NPC94139
0.8421	Intermediate Similarity	NPC147284
0.825	Intermediate Similarity	NPC210497
0.8158	Intermediate Similarity	NPC487735
0.7297	Intermediate Similarity	NPC3358
0.7297	Intermediate Similarity	NPC306884
0.7297	Intermediate Similarity	NPC603092
0.7143	Intermediate Similarity	NPC610566
0.6977	Remote Similarity	NPC192
0.6585	Remote Similarity	NPC487736
0.641	Remote Similarity	NPC76938
0.641	Remote Similarity	NPC32714
0.6111	Remote Similarity	NPC606762
0.6098	Remote Similarity	NPC53051
0.6098	Remote Similarity	NPC24404
0.6098	Remote Similarity	NPC313030
0.5952	Remote Similarity	NPC146798
0.5952	Remote Similarity	NPC222522
0.5952	Remote Similarity	NPC106396
0.5952	Remote Similarity	NPC94351
0.5952	Remote Similarity	NPC168303
0.5909	Remote Similarity	NPC302219
0.5814	Remote Similarity	NPC196479
0.575	Remote Similarity	NPC25493
0.5714	Remote Similarity	NPC177420
0.561	Remote Similarity	NPC470700
0.561	Remote Similarity	NPC54844
0.561	Remote Similarity	NPC39097
0.561	Remote Similarity	NPC302681
0.561	Remote Similarity	NPC118286
0.561	Remote Similarity	NPC109691
0.5581	Remote Similarity	NPC55561
0.5556	Remote Similarity	NPC71002
0.5556	Remote Similarity	NPC249828
0.5429	Remote Similarity	NPC27974
0.5349	Remote Similarity	NPC39664
0.5333	Remote Similarity	NPC166761
0.5238	Remote Similarity	NPC113460
0.5217	Remote Similarity	NPC129373
0.5217	Remote Similarity	NPC242342
0.5217	Remote Similarity	NPC85479
0.5208	Remote Similarity	NPC48730
0.5208	Remote Similarity	NPC294741
0.5128	Remote Similarity	NPC242240
0.5111	Remote Similarity	NPC232523
0.5106	Remote Similarity	NPC158253

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC487734 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4889
0.1-0.2	3999
0.2-0.3	242
0.3-0.4	19
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