NPASS Compound

Natural Product: NPC482472

Natural Product ID	NPC482472
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	MDDPZOZWEZNMTK-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	12314021
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0002991] Hydroxyflavonoids [CHEMONTID:0002993] 7-hydroxyflavonoids

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 33 35 0 0 0 0 0 0 0 0999 V2000 2.6304 -0.8156 1.0546 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9641 -1.0159 0.7156 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5913 -0.1485 -0.1559 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8882 0.9091 -0.6823 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5649 1.0885 -0.3317 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9116 0.2424 0.5337 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4945 0.4596 0.8892 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0996 1.5155 0.0173 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5799 1.6986 0.2700 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2258 0.3842 0.1047 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5282 0.3036 -0.3405 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1734 -0.9109 -0.5108 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5094 -2.0911 -0.2316 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.2091 -2.0031 0.2125 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5469 -0.7784 0.3882 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2451 -0.7372 0.8350 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1642 -3.2984 -0.4056 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.1857 1.4903 -0.6177 O 0 0 0 0 0 0 0 0 0 0 0 0 5.9409 -0.3494 -0.5003 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1945 -1.5279 1.7414 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5533 -1.8334 1.1058 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3731 1.6100 -1.3786 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0391 1.9320 -0.7652 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4834 0.8252 1.9428 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0573 1.3065 -1.0563 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3740 2.5025 0.2460 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9524 2.4804 -0.3878 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6930 2.0551 1.3323 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2145 -0.9473 -0.8679 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6768 -2.9277 0.4354 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5264 -3.8112 0.4040 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8409 2.2254 -1.1873 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3107 0.1669 -1.2913 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 3 4 2 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 2 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 13 17 1 0 11 18 1 0 3 19 1 0 6 1 1 0 16 7 1 0 15 10 1 0 1 20 1 0 2 21 1 0 4 22 1 0 5 23 1 0 7 24 1 0 8 25 1 0 8 26 1 0 9 27 1 0 9 28 1 0 12 29 1 0 14 30 1 0 17 31 1 0 18 32 1 0 19 33 1 0 M END

Standard InCHIKey	MDDPZOZWEZNMTK-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C15H14O4/c16-10-3-1-9(2-4-10)14-6-5-12-13(18)7-11(17)8-15(12)19-14/h1-4,7-8,14,16-18H,5-6H2
SMILES	c1cc(ccc1C1CCc2c(cc(cc2O1)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
NPO40849	Faramea guianesis	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[8201315]

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
Inhibition	3
Survival	1

Activity Type	# Activity
Organism	4

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
NPT634	Organism	Leishmania amazonensis	Leishmania amazonensis	Inhibition	=	57.0	%	PMID[8201315]
NPT634	Organism	Leishmania amazonensis	Leishmania amazonensis	Inhibition	=	100.0	%	PMID[8201315]

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT634	Organism	Leishmania amazonensis	Leishmania amazonensis	Survival	=	0.0	%	PMID[8201315]

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 NPC482472 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	25067
0.1-0.2	20089
0.2-0.3	3851
0.3-0.4	649
0.4-0.5	162
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
0.6667	Remote Similarity	NPC93398
0.6667	Remote Similarity	NPC258979
0.6667	Remote Similarity	NPC8283
0.6458	Remote Similarity	NPC207179
0.6458	Remote Similarity	NPC167571
0.6458	Remote Similarity	NPC278552
0.6078	Remote Similarity	NPC17809
0.6	Remote Similarity	NPC32441
0.6	Remote Similarity	NPC79943
0.5667	Remote Similarity	NPC277331
0.5667	Remote Similarity	NPC100482
0.56	Remote Similarity	NPC76465
0.5577	Remote Similarity	NPC261619
0.5577	Remote Similarity	NPC61477
0.5577	Remote Similarity	NPC188022
0.5577	Remote Similarity	NPC78770
0.5577	Remote Similarity	NPC219876
0.5577	Remote Similarity	NPC126029
0.5577	Remote Similarity	NPC15658
0.5469	Remote Similarity	NPC82330
0.54	Remote Similarity	NPC106914
0.54	Remote Similarity	NPC86502
0.5385	Remote Similarity	NPC100099
0.5385	Remote Similarity	NPC66384
0.5385	Remote Similarity	NPC36016
0.5192	Remote Similarity	NPC268266
0.5192	Remote Similarity	NPC42760
0.5192	Remote Similarity	NPC220825
0.5192	Remote Similarity	NPC268342
0.5167	Remote Similarity	NPC156818
0.5147	Remote Similarity	NPC287884
0.5147	Remote Similarity	NPC8704
0.5098	Remote Similarity	NPC329225
0.5098	Remote Similarity	NPC147686
0.5094	Remote Similarity	NPC295261
0.5094	Remote Similarity	NPC296490
0.5088	Remote Similarity	NPC16435
0.5088	Remote Similarity	NPC171932

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC482472 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4478
0.1-0.2	4513
0.2-0.3	143
0.3-0.4	9
0.4-0.5	3
0.5-0.6	3
0.6-0.7	1
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
0.6	Remote Similarity	NPD1552	Clinical (unspecified phase)
0.5577	Remote Similarity	NPD1612	Clinical (unspecified phase)
0.5577	Remote Similarity	NPD1613	Phase 4
0.5098	Remote Similarity	NPD1549	Phase 2

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