NPASS Compound

Natural Product: NPC486126

Natural Product ID	NPC486126
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ZDVIABVNEDLARA-VWCMKLTGSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	127026640
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001013] Steroidal 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 81 86 0 0 0 0 0 0 0 0999 V2000 6.7970 -1.9124 1.5452 C 0 0 0 0 0 0 0 0 0 0 0 0 5.8552 -0.9719 0.8167 C 0 0 1 0 0 0 0 0 0 0 0 0 6.4053 0.4237 0.7280 C 0 0 1 0 0 0 0 0 0 0 0 0 6.5451 0.9049 -0.6960 C 0 0 2 0 0 0 0 0 0 0 0 0 5.3329 0.5677 -1.5327 C 0 0 1 0 0 0 0 0 0 0 0 0 4.7165 -0.7419 -1.1755 C 0 0 1 0 0 0 0 0 0 0 0 0 5.5913 -1.5259 -0.4302 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5123 -0.5261 -0.5295 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4233 -1.0803 -1.2001 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7622 -2.0482 -0.2684 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2398 -1.9820 -0.3335 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2152 -0.6429 0.1360 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6584 0.4621 -0.4144 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.1005 1.6674 -0.8564 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2303 2.0781 0.0311 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0201 0.9075 0.5786 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.6327 -0.3066 -0.2268 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5927 -1.4406 -0.0876 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5154 -1.1589 1.0944 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3785 0.0481 0.8705 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.1943 0.2424 2.1428 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2659 0.0008 -0.3138 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.4211 1.4993 -0.6372 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9628 1.9026 -0.6534 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4658 1.2257 0.5987 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.6792 2.1399 1.6505 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5890 -0.6196 -0.1217 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7910 -0.0517 -0.1947 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8278 -1.0316 0.0610 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.0861 -0.8641 0.0785 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.2298 -2.2338 0.2948 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8255 -2.0382 0.2071 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4313 -0.0463 -1.6394 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3725 1.5997 -1.4509 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7063 0.4385 -1.2966 O 0 0 0 0 0 0 0 0 0 0 0 0 8.5187 1.5161 -1.6273 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6405 1.3141 1.4904 O 0 0 0 0 0 0 0 0 0 0 0 0 6.4246 -2.9434 1.4100 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8061 -1.7728 1.1173 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8625 -1.6723 2.6241 H 0 0 0 0 0 0 0 0 0 0 0 0 4.9134 -0.9420 1.4062 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4211 0.4158 1.1758 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6026 2.0089 -0.6537 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6579 0.5532 -2.5934 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4890 -1.3279 -2.1032 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8269 -1.5692 -2.1135 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0423 -3.0761 -0.6154 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0614 -1.9577 0.7812 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1538 -2.2474 -1.3218 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0946 -2.8037 0.3665 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1319 -0.6261 1.2587 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4361 0.7273 0.3304 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4264 1.5369 -1.9142 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6248 2.5300 -0.8826 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8434 2.7147 0.8700 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8792 2.7526 -0.5633 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6610 0.7551 1.6228 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6352 0.0083 -1.3047 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0847 -2.4093 0.1729 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1658 -1.6649 -1.0137 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8091 -0.8745 1.9324 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0314 -2.0455 1.4479 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2646 1.3330 2.3924 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.2264 -0.1094 2.0467 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6972 -0.2249 3.0181 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7771 -0.4317 -1.2042 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9236 1.6535 -1.5918 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9010 2.0184 0.2170 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5145 1.4922 -1.5755 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8849 3.0136 -0.5917 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2978 2.8437 1.3988 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.9226 0.9982 -0.4166 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3759 -2.6809 -0.5776 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3275 -2.3323 1.1569 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8495 0.7943 -2.1902 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6745 -0.5680 -2.2727 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4134 2.0289 -0.5623 H 0 0 0 0 0 0 0 0 0 0 0 0 8.0118 2.2137 -2.3358 H 0 0 0 0 0 0 0 0 0 0 0 0 9.4475 1.1907 -2.1248 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7774 2.1187 -0.7253 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2020 0.8627 2.2515 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 1 0 5 6 1 0 6 7 1 0 6 8 1 0 8 9 1 0 9 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 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 1 20 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 1 22 27 1 0 27 28 2 0 28 29 1 0 29 30 2 0 29 31 1 0 31 32 1 0 13 33 1 0 5 34 1 0 4 35 1 0 35 36 1 0 3 37 1 0 7 2 1 0 33 9 1 0 17 12 1 0 25 20 1 0 32 27 1 0 25 16 1 0 1 38 1 0 1 39 1 0 1 40 1 0 2 41 1 1 3 42 1 1 4 43 1 1 5 44 1 6 6 45 1 6 9 46 1 6 10 47 1 0 10 48 1 0 11 49 1 0 11 50 1 0 12 51 1 1 13 52 1 1 14 53 1 0 14 54 1 0 15 55 1 0 15 56 1 0 16 57 1 1 17 58 1 6 18 59 1 0 18 60 1 0 19 61 1 0 19 62 1 0 21 63 1 0 21 64 1 0 21 65 1 0 22 66 1 6 23 67 1 0 23 68 1 0 24 69 1 0 24 70 1 0 26 71 1 0 28 72 1 0 32 73 1 0 32 74 1 0 33 75 1 0 33 76 1 0 34 77 1 0 36 78 1 0 36 79 1 0 36 80 1 0 37 81 1 0 M END

Standard InCHIKey	ZDVIABVNEDLARA-VWCMKLTGSA-N
Standard InCHI	InChI=1S/C29H44O8/c1-15-24(31)26(34-3)25(32)27(36-15)37-18-5-6-19-16(12-18)4-7-22-20(19)8-10-28(2)21(9-11-29(22,28)33)17-13-23(30)35-14-17/h13,15-16,18-22,24-27,31-33H,4-12,14H2,1-3H3/t15-,16+,18-,19-,20+,21+,22+,24-,25-,26+,27-,28+,29-/m0/s1
SMILES	C[C@H]1[C@@H]([C@H]([C@@H]([C@@H](O1)O[C@H]1CC[C@H]2[C@H](CC[C@@H]3[C@@H]2CC[C@]2(C)[C@H](CC[C@]32O)C2=CC(=O)OC2)C1)O)OC)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
NPO8402	Thevetia peruviana	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26714048]
NPO8402	Thevetia peruviana	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[39027575]
NPO8402	Thevetia peruviana	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO8402	Thevetia peruviana	Species	Apocynaceae	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	4

Activity Type	# Activity
Cell line	1
Non-molecular	2
Others	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
NPT1312	Cell line	SW1990	Homo sapiens	IC50	=	530.0	nM	PMID[26714048]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	=	210.0	nM	PMID[26714048]
NPT20529	Non-molecular	NON-PROTEIN TARGET	n.a.	IC50	=	570.0	nM	PMID[26714048]
NPT27	Others	Unspecified	n.a.	IC50	>	10000.0	nM	PMID[26714048]

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 NPC486126 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	10215
0.1-0.2	35687
0.2-0.3	3676
0.3-0.4	90
0.4-0.5	121
0.5-0.6	51
0.6-0.7	5
0.7-0.8	1
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
0.7564	Intermediate Similarity	NPC486129
0.7375	Intermediate Similarity	NPC199428
0.7375	Intermediate Similarity	NPC109448
0.7375	Intermediate Similarity	NPC310341
0.7284	Intermediate Similarity	NPC250556
0.7195	Intermediate Similarity	NPC305574
0.7011	Intermediate Similarity	NPC486127
0.6705	Remote Similarity	NPC486151
0.6559	Remote Similarity	NPC486128
0.6374	Remote Similarity	NPC55532
0.6047	Remote Similarity	NPC479356
0.6047	Remote Similarity	NPC479355
0.5789	Remote Similarity	NPC469749
0.5747	Remote Similarity	NPC309034
0.5652	Remote Similarity	NPC5883
0.5632	Remote Similarity	NPC99620
0.5618	Remote Similarity	NPC84949
0.5618	Remote Similarity	NPC480562
0.5618	Remote Similarity	NPC74945
0.5618	Remote Similarity	NPC31354
0.5618	Remote Similarity	NPC69576
0.5506	Remote Similarity	NPC6108
0.5506	Remote Similarity	NPC469750
0.5506	Remote Similarity	NPC89514
0.5495	Remote Similarity	NPC483822
0.5495	Remote Similarity	NPC93883
0.5474	Remote Similarity	NPC480910
0.5474	Remote Similarity	NPC480909
0.5444	Remote Similarity	NPC76572
0.5444	Remote Similarity	NPC193382
0.5385	Remote Similarity	NPC180079
0.5333	Remote Similarity	NPC17896
0.5333	Remote Similarity	NPC469755
0.5333	Remote Similarity	NPC284406
0.5333	Remote Similarity	NPC34390
0.5333	Remote Similarity	NPC197707
0.5333	Remote Similarity	NPC251866
0.5312	Remote Similarity	NPC486130
0.5281	Remote Similarity	NPC479351
0.5281	Remote Similarity	NPC99728
0.5281	Remote Similarity	NPC87250
0.5281	Remote Similarity	NPC244402
0.5281	Remote Similarity	NPC479352
0.5281	Remote Similarity	NPC50305
0.5222	Remote Similarity	NPC196429
0.5208	Remote Similarity	NPC27363
0.5204	Remote Similarity	NPC486143
0.5204	Remote Similarity	NPC486135
0.5204	Remote Similarity	NPC486142
0.5204	Remote Similarity	NPC486137
0.5204	Remote Similarity	NPC486149
0.5165	Remote Similarity	NPC5311
0.5165	Remote Similarity	NPC157376
0.5165	Remote Similarity	NPC77299
0.5165	Remote Similarity	NPC480906
0.5165	Remote Similarity	NPC142066
0.5165	Remote Similarity	NPC603972
0.5152	Remote Similarity	NPC232785
0.5152	Remote Similarity	NPC486139
0.5111	Remote Similarity	NPC471633
0.5109	Remote Similarity	NPC10823
0.5109	Remote Similarity	NPC480914
0.5055	Remote Similarity	NPC219085

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC486126 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	5280
0.1-0.2	3757
0.2-0.3	99
0.3-0.4	0
0.4-0.5	11
0.5-0.6	1
0.6-0.7	0
0.7-0.8	1
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
0.7284	Intermediate Similarity	NPD7507	Pre-clinical
0.5333	Remote Similarity	NPD7319	Approved

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