NPASS Compound

Natural Product: NPC479031

Natural Product ID	NPC479031
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	UHNLNJVDLFIIBG-KFPNGALKSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	11801098
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000253] Stilbenes [CHEMONTID:0000142] Stilbene glycosides

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 74 77 0 0 0 0 0 0 0 0999 V2000 3.5262 9.2023 -1.5461 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2193 8.7470 -1.3187 O 0 0 0 0 0 0 0 0 0 0 0 0 1.9530 7.4072 -1.1250 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6935 6.9041 -0.8995 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4894 5.5437 -0.7122 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5211 4.6672 -0.7444 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3424 3.2233 -0.5514 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2149 2.6199 -0.3339 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0947 1.1718 -0.1486 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2054 0.6884 0.0821 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3940 -0.6431 0.2612 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2570 -1.4930 0.2064 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0063 -1.0519 -0.0144 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1699 0.3285 -0.1957 C 0 0 0 0 0 0 0 0 0 0 0 0 2.0911 -1.8937 -0.0628 O 0 0 0 0 0 0 0 0 0 0 0 0 2.1506 -3.2615 0.0962 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5797 -3.9407 -1.2057 C 0 0 1 0 0 0 0 0 0 0 0 0 3.9181 -3.4496 -1.6783 C 0 0 2 0 0 0 0 0 0 0 0 0 4.6961 -2.9998 -0.4572 C 0 0 1 0 0 0 0 0 0 0 0 0 4.2949 -3.9391 0.6777 C 0 0 1 0 0 0 0 0 0 0 0 0 5.2989 -3.7973 1.8128 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9314 -4.7050 2.8075 O 0 0 0 0 0 0 0 0 0 0 0 0 3.0221 -3.6663 1.1104 O 0 0 0 0 0 0 0 0 0 0 0 0 6.0758 -3.0361 -0.6766 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7685 -2.3040 -2.4780 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5165 -5.3151 -1.0411 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6148 -1.2125 0.4907 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8196 -0.5349 0.5846 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.6632 -0.9733 -0.5963 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.5574 -2.1269 -0.3585 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.9800 -2.3022 1.0596 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.7224 -0.9650 1.7556 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.3477 -0.9733 3.1434 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7355 -1.1104 3.0079 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3570 -0.8337 1.8206 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.2839 -2.7240 1.1833 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9205 -3.2821 -0.8739 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.4165 0.1193 -1.0225 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7902 5.1699 -0.9711 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0010 6.5040 -1.1565 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2235 8.8773 -0.7272 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9388 8.7877 -2.4833 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5292 10.3017 -1.5626 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1359 7.5735 -0.8687 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5262 5.1997 -0.5380 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2403 2.5953 -0.5938 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6832 3.2492 -0.2905 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0143 1.3815 0.1098 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4620 -2.5411 0.3552 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1650 0.6824 -0.3703 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1683 -3.6864 0.3389 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8346 -3.6879 -1.9958 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4827 -4.2279 -2.2405 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4570 -1.9563 -0.1676 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4158 -4.9699 0.2822 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2790 -4.1404 1.4174 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4041 -2.7720 2.1719 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7112 -5.0496 3.3142 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3483 -3.7952 -1.2591 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3068 -2.5058 -3.3128 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9994 -5.5558 -0.2083 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6624 0.5806 0.5214 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9652 -1.1875 -1.4465 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4883 -1.9819 -0.9815 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2427 -3.0098 1.5333 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1348 -0.1568 1.1312 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9123 -1.8214 3.6899 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1592 -0.0064 3.6459 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2147 -0.8450 3.8204 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2954 -3.4463 1.8786 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5490 -3.7942 -1.4275 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7487 0.8009 -1.3416 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6134 4.4580 -0.9945 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9860 6.8877 -1.3322 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 2 0 13 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 20 23 1 0 19 24 1 0 18 25 1 0 17 26 1 0 11 27 1 0 27 28 1 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 32 35 1 0 31 36 1 0 30 37 1 0 29 38 1 0 6 39 1 0 39 40 2 0 40 3 1 0 14 9 1 0 23 16 1 0 35 28 1 0 1 41 1 0 1 42 1 0 1 43 1 0 4 44 1 0 5 45 1 0 7 46 1 0 8 47 1 0 10 48 1 0 12 49 1 0 14 50 1 0 16 51 1 1 17 52 1 6 18 53 1 6 19 54 1 1 20 55 1 6 21 56 1 0 21 57 1 0 22 58 1 0 24 59 1 0 25 60 1 0 26 61 1 0 28 62 1 1 29 63 1 6 30 64 1 6 31 65 1 1 32 66 1 6 33 67 1 0 33 68 1 0 34 69 1 0 36 70 1 0 37 71 1 0 38 72 1 0 39 73 1 0 40 74 1 0 M END

Standard InCHIKey	UHNLNJVDLFIIBG-KFPNGALKSA-N
Standard InCHI	InChI=1S/C27H34O13/c1-36-15-6-4-13(5-7-15)2-3-14-8-16(37-26-24(34)22(32)20(30)18(11-28)39-26)10-17(9-14)38-27-25(35)23(33)21(31)19(12-29)40-27/h2-10,18-35H,11-12H2,1H3/b3-2+/t18-,19-,20-,21-,22+,23+,24-,25-,26-,27-/m1/s1
SMILES	COc1ccc(/C=C/c2cc(cc(c2)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)O[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)cc1

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
NPO20665	Erythrophleum lasianthum	Species	Fabaceae	Eukaryota	Seeds	n.a.	n.a.	PMID[9392877]
NPO20665	Erythrophleum lasianthum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO20665	Erythrophleum lasianthum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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	2

Activity Type	# Activity
Cell line	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
NPT20967	Cell line	Platelet	n.a.	IC50	=	112.8	ug	PMID[9392877]
NPT20967	Cell line	Platelet	n.a.	IC50	=	300.0	ug	PMID[9392877]

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 NPC479031 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	17248
0.1-0.2	27699
0.2-0.3	3846
0.3-0.4	675
0.4-0.5	294
0.5-0.6	62
0.6-0.7	22
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC479028
0.7593	Intermediate Similarity	NPC214910
0.7544	Intermediate Similarity	NPC294166
0.7544	Intermediate Similarity	NPC115022
0.6842	Remote Similarity	NPC479029
0.6833	Remote Similarity	NPC479030
0.6667	Remote Similarity	NPC26080
0.6667	Remote Similarity	NPC165686
0.6481	Remote Similarity	NPC200092
0.6349	Remote Similarity	NPC98777
0.629	Remote Similarity	NPC604095
0.6271	Remote Similarity	NPC248355
0.6207	Remote Similarity	NPC604356
0.6167	Remote Similarity	NPC55040
0.6154	Remote Similarity	NPC212729
0.6154	Remote Similarity	NPC604498
0.6066	Remote Similarity	NPC302378
0.6066	Remote Similarity	NPC85799
0.6066	Remote Similarity	NPC303422
0.6066	Remote Similarity	NPC218003
0.6038	Remote Similarity	NPC269242
0.6034	Remote Similarity	NPC218685
0.6032	Remote Similarity	NPC37468
0.6032	Remote Similarity	NPC8497
0.6	Remote Similarity	NPC295970
0.6	Remote Similarity	NPC609376
0.5965	Remote Similarity	NPC166040
0.5932	Remote Similarity	NPC251102
0.5932	Remote Similarity	NPC210298
0.5926	Remote Similarity	NPC153149
0.5926	Remote Similarity	NPC294470
0.5849	Remote Similarity	NPC276195
0.5846	Remote Similarity	NPC212770
0.5846	Remote Similarity	NPC475084
0.5818	Remote Similarity	NPC25817
0.5741	Remote Similarity	NPC217854
0.5714	Remote Similarity	NPC60589
0.5714	Remote Similarity	NPC469708
0.5667	Remote Similarity	NPC472024
0.5667	Remote Similarity	NPC270849
0.5636	Remote Similarity	NPC192810
0.5625	Remote Similarity	NPC242028
0.5625	Remote Similarity	NPC203230
0.5574	Remote Similarity	NPC26653
0.5574	Remote Similarity	NPC80600
0.5574	Remote Similarity	NPC210478
0.5556	Remote Similarity	NPC59324
0.5517	Remote Similarity	NPC221090
0.5517	Remote Similarity	NPC80098
0.5507	Remote Similarity	NPC185103
0.55	Remote Similarity	NPC49074
0.5479	Remote Similarity	NPC93924
0.5439	Remote Similarity	NPC299144
0.541	Remote Similarity	NPC162093
0.541	Remote Similarity	NPC23084
0.5397	Remote Similarity	NPC104167
0.5385	Remote Similarity	NPC276753
0.5385	Remote Similarity	NPC205796
0.5385	Remote Similarity	NPC228907
0.5373	Remote Similarity	NPC210192
0.5345	Remote Similarity	NPC608788
0.5323	Remote Similarity	NPC481303
0.5312	Remote Similarity	NPC232673
0.5303	Remote Similarity	NPC246947
0.5303	Remote Similarity	NPC185778
0.5273	Remote Similarity	NPC142319
0.5254	Remote Similarity	NPC69513
0.5254	Remote Similarity	NPC145900
0.5238	Remote Similarity	NPC473044
0.5231	Remote Similarity	NPC100389
0.5211	Remote Similarity	NPC488085
0.5208	Remote Similarity	NPC82016
0.5205	Remote Similarity	NPC607190
0.5167	Remote Similarity	NPC48863
0.5167	Remote Similarity	NPC251981
0.5167	Remote Similarity	NPC13745
0.5152	Remote Similarity	NPC252169
0.5152	Remote Similarity	NPC65530
0.5147	Remote Similarity	NPC248119
0.5139	Remote Similarity	NPC3293
0.5085	Remote Similarity	NPC12308
0.5085	Remote Similarity	NPC226712
0.5082	Remote Similarity	NPC310661
0.5082	Remote Similarity	NPC215833
0.5082	Remote Similarity	NPC9912
0.5077	Remote Similarity	NPC473045
0.5075	Remote Similarity	NPC186418
0.5072	Remote Similarity	NPC259767

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC479031 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4243
0.1-0.2	4701
0.2-0.3	188
0.3-0.4	17
0.4-0.5	0
0.5-0.6	1
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
0.5085	Remote Similarity	NPD1091	Pre-clinical

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