NPASS Compound

Natural Product: NPC488655

Natural Product ID	NPC488655
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	IOILMHODHQIOKP-OFMBRRDOSA-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]

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 77 79 0 0 0 0 0 0 0 0999 V2000 -5.4734 4.3617 -0.3835 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1892 3.0972 -0.4058 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9232 2.5800 0.0343 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6563 1.2464 -0.0028 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3856 0.6857 0.4330 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6000 -0.1293 -0.5504 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.4276 0.9347 -1.6725 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1939 -1.3008 -1.1741 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5756 -1.7307 -0.6864 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4051 -2.5781 -1.2502 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0522 -2.4627 -0.9104 C 0 0 1 0 0 0 0 0 0 0 0 0 0.1253 -1.7486 0.4025 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5491 -1.7110 0.9223 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5063 -0.9657 0.4341 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2023 -0.1007 -0.6928 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8076 0.3890 -0.6903 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2302 -0.3366 0.1139 C 0 0 1 0 0 0 0 0 0 0 0 0 3.1322 1.0025 -0.6487 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1162 1.1988 -1.5918 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1851 0.3547 -2.5320 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0751 2.3335 -1.5492 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8423 2.2062 -0.2312 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2373 3.6067 -1.5425 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2245 4.7734 -1.4988 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5595 -2.6678 2.0629 C 0 0 1 0 0 0 0 0 0 0 0 0 2.6117 -2.4919 2.9236 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2312 -3.7508 3.0809 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3306 -2.2592 2.6475 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.4820 -2.4805 1.4898 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7655 -2.3452 1.9016 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6112 -3.3971 2.0883 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1638 -4.5682 1.8613 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0233 -3.2940 2.5381 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5974 -3.7400 -0.8608 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8215 3.4202 0.5673 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8415 5.1761 -0.0508 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4636 4.7267 -0.7319 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9480 2.4144 -0.7743 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4966 0.6856 -0.3887 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5458 0.2225 1.4125 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7062 1.5646 0.6695 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.2415 0.4478 -2.6520 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8241 1.7709 -1.3955 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4603 1.3824 -1.8630 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4126 -1.0918 -2.2788 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6719 -2.8661 -0.6765 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8144 -1.4358 0.3225 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3992 -1.4339 -1.3638 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3894 -3.0284 -2.2957 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8921 -3.4332 -0.6889 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4995 -1.8943 -1.7625 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5261 -0.9796 0.8528 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5106 -0.6594 -1.6202 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5503 0.3864 -1.7970 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8659 1.4739 -0.3542 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1976 0.1675 1.1310 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7411 2.2885 -2.4122 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0607 1.1423 -0.0069 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2634 2.6112 0.6100 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8184 2.7277 -0.3020 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6605 3.6220 -2.4693 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5635 3.6357 -0.6655 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7005 5.6745 -1.8251 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1080 4.5542 -2.1307 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5778 4.9137 -0.4430 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4442 -3.7201 1.7038 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0883 -3.7092 3.7558 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4337 -4.4564 3.3959 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5231 -4.0558 2.0457 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2790 -3.5864 1.3137 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1796 -4.1491 3.2584 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7417 -3.4722 1.7203 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2225 -2.3366 3.0614 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0504 -4.4485 -1.0802 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5708 3.1199 1.6118 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9196 3.4328 -0.0959 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1259 4.4836 0.6325 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 6 5 1 1 6 7 1 0 6 8 1 0 8 9 1 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 1 13 14 2 0 14 15 1 0 15 16 1 0 16 17 1 0 15 18 1 0 18 19 1 0 19 20 2 0 19 21 1 0 21 22 1 0 21 23 1 0 23 24 1 0 13 25 1 0 25 26 1 0 26 27 1 0 25 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 2 0 31 33 1 0 11 34 1 0 3 35 1 0 17 6 1 0 17 12 1 0 29 12 1 0 1 36 1 0 1 37 1 0 2 38 1 0 4 39 1 0 5 40 1 0 5 41 1 0 7 42 1 0 7 43 1 0 7 44 1 0 8 45 1 6 9 46 1 0 9 47 1 0 9 48 1 0 10 49 1 0 10 50 1 0 11 51 1 6 14 52 1 0 15 53 1 6 16 54 1 0 16 55 1 0 17 56 1 1 21 57 1 0 22 58 1 0 22 59 1 0 22 60 1 0 23 61 1 0 23 62 1 0 24 63 1 0 24 64 1 0 24 65 1 0 25 66 1 6 27 67 1 0 27 68 1 0 27 69 1 0 29 70 1 6 33 71 1 0 33 72 1 0 33 73 1 0 34 74 1 0 35 75 1 0 35 76 1 0 35 77 1 0 M END

Standard InCHIKey	IOILMHODHQIOKP-OFMBRRDOSA-N
Standard InCHI	InChI=1S/C28H42O7/c1-9-16(3)11-12-27(7)18(5)13-23(30)28-21(25(32-8)35-26(28)33-19(6)29)14-20(15-22(27)28)34-24(31)17(4)10-2/h9,11,14,17-18,20,22-23,25-26,30H,1,10,12-13,15H2,2-8H3/b16-11+/t17?,18-,20+,22+,23+,25+,26-,27-,28-/m1/s1
SMILES	C=C/C(=C/C[C@]1(C)[C@H](C)C[C@@H]([C@@]23C(=C[C@@H](C[C@@H]12)OC(=O)C(C)CC)[C@@H](OC)O[C@H]3OC(=O)C)O)/C

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
NPO40063	Casearia graveolens	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26474353]
NPO40063	Casearia graveolens	Species	Salicaceae	Eukaryota	Leaves	n.a.	n.a.	PMID[31916761]

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
NPT81	Cell line	A549	Homo sapiens	IC50	>	10000.0	nM	PMID[31916761]
NPT65	Cell line	HepG2	Homo sapiens	IC50	>	10000.0	nM	PMID[31916761]

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 NPC488655 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	17115
0.1-0.2	28617
0.2-0.3	3980
0.3-0.4	44
0.4-0.5	39
0.5-0.6	20
0.6-0.7	14
0.7-0.8	0
0.8-0.85	2
0.85-0.9	7
0.9-0.95	6
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC488658
0.9333	High Similarity	NPC330003
0.9333	High Similarity	NPC470321
0.9333	High Similarity	NPC264867
0.9333	High Similarity	NPC473207
0.9167	High Similarity	NPC488660
0.9167	High Similarity	NPC488657
0.8983	High Similarity	NPC488659
0.8983	High Similarity	NPC604149
0.8548	High Similarity	NPC134270
0.8548	High Similarity	NPC329623
0.8548	High Similarity	NPC488654
0.8548	High Similarity	NPC609880
0.8525	High Similarity	NPC488656
0.8361	Intermediate Similarity	NPC602188
0.8154	Intermediate Similarity	NPC252296
0.7969	Intermediate Similarity	NPC201880
0.7969	Intermediate Similarity	NPC81567
0.7969	Intermediate Similarity	NPC488652
0.7969	Intermediate Similarity	NPC609711
0.7937	Intermediate Similarity	NPC488653
0.7846	Intermediate Similarity	NPC238397
0.7846	Intermediate Similarity	NPC609715
0.7612	Intermediate Similarity	NPC488964
0.7612	Intermediate Similarity	NPC184512
0.7313	Intermediate Similarity	NPC475889
0.7313	Intermediate Similarity	NPC7613
0.7313	Intermediate Similarity	NPC479942
0.7101	Intermediate Similarity	NPC471363
0.6901	Remote Similarity	NPC127933
0.6711	Remote Similarity	NPC109376
0.6667	Remote Similarity	NPC116292
0.6667	Remote Similarity	NPC479491
0.6528	Remote Similarity	NPC119550
0.6377	Remote Similarity	NPC479943
0.6286	Remote Similarity	NPC473204
0.6232	Remote Similarity	NPC488235
0.6197	Remote Similarity	NPC311223
0.6197	Remote Similarity	NPC479940
0.6197	Remote Similarity	NPC7644
0.6197	Remote Similarity	NPC316974
0.6197	Remote Similarity	NPC479497
0.6027	Remote Similarity	NPC479941
0.5672	Remote Similarity	NPC604446
0.5634	Remote Similarity	NPC600724
0.5625	Remote Similarity	NPC179128
0.5584	Remote Similarity	NPC40728
0.5493	Remote Similarity	NPC606965
0.5488	Remote Similarity	NPC486751
0.5455	Remote Similarity	NPC125423
0.5429	Remote Similarity	NPC603601
0.5341	Remote Similarity	NPC320734
0.5301	Remote Similarity	NPC316708
0.5294	Remote Similarity	NPC224660
0.5244	Remote Similarity	NPC87630
0.5244	Remote Similarity	NPC473216
0.5135	Remote Similarity	NPC88507
0.507	Remote Similarity	NPC470297
0.5067	Remote Similarity	NPC472188
0.5065	Remote Similarity	NPC217921
0.5065	Remote Similarity	NPC88013
0.5065	Remote Similarity	NPC135015
0.5065	Remote Similarity	NPC218158

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC488655 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6931
0.1-0.2	2188
0.2-0.3	31
0.3-0.4	0
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