NPASS Compound

Natural Product: NPC196839

Natural Product ID	NPC196839
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	LPMXVESGRSUGHW-PCZRPPSHSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	52931492
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0001125] Steroid lactones [CHEMONTID:0001555] Cardenolides and derivatives [CHEMONTID:0001559] Cardenolide glycosides and derivatives

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 85 90 0 0 0 0 0 0 0 0999 V2000 7.0558 0.2993 2.4467 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4827 -0.8944 1.7034 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2556 -1.2387 0.4788 C 0 0 1 0 0 0 0 0 0 0 0 0 6.9727 -0.3810 -0.7073 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6520 0.3146 -0.5829 C 0 0 1 0 0 0 0 0 0 0 0 0 4.7274 -0.5850 0.2195 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1482 -0.6777 1.5194 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4561 -0.0117 0.2204 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5049 -0.8633 -0.3884 C 0 0 1 0 0 0 0 0 0 0 0 0 1.5450 -1.2652 0.6834 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8176 -0.0169 1.1301 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0809 0.7098 0.0653 C 0 0 2 0 0 0 0 0 0 0 0 0 0.4871 2.1800 0.1140 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2235 2.8114 1.2885 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4011 0.5191 0.2172 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.1752 0.8927 -1.0485 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8842 -0.0686 -2.1547 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5465 -0.7350 -1.8843 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4584 0.2669 -1.3487 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8595 -0.1743 -1.5176 C 0 0 0 0 0 0 0 0 0 0 0 0 0.3372 1.3772 -2.2312 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.6210 1.1577 -0.8118 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.5161 0.6805 -1.9469 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2994 -0.5057 -1.4230 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6273 -0.8944 -0.1224 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.6953 -1.4965 0.7652 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.8917 -1.8589 0.3557 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6328 -2.3905 1.4864 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.8093 -2.8432 1.5186 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.8079 -2.3212 2.5823 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.5902 -1.7751 2.1966 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2217 0.4773 0.3816 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.5204 1.2155 0.7068 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3846 0.4660 1.6033 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0504 1.1919 1.3488 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4172 1.2099 2.5611 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8967 2.5383 -0.6527 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8022 0.8087 1.7160 O 0 0 0 0 0 0 0 0 0 0 0 0 5.8483 1.5212 0.0743 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9483 -1.2229 -1.8424 O 0 0 0 0 0 0 0 0 0 0 0 0 8.6254 -1.0820 0.7894 O 0 0 0 0 0 0 0 0 0 0 0 0 7.8374 0.8191 1.8385 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5628 0.0072 3.3894 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2550 1.0161 2.7483 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5808 -1.7703 2.4109 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1347 -2.3190 0.2483 H 0 0 0 0 0 0 0 0 0 0 0 0 7.7547 0.3758 -0.9178 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2377 0.4715 -1.6014 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7102 -1.5788 -0.2571 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0637 -1.7762 -0.7027 H 0 0 0 0 0 0 0 0 0 0 0 0 2.1705 -1.5748 1.5732 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9035 -2.1079 0.4577 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1887 -0.3580 1.9900 H 0 0 0 0 0 0 0 0 0 0 0 0 0.1035 2.7214 -0.7884 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6065 2.1709 -0.0239 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9346 3.3869 1.6431 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5575 -0.5867 0.3259 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7380 1.8935 -1.3474 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.6130 -0.9131 -2.2337 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7922 0.4803 -3.1193 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1578 -1.0565 -2.8774 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7094 -1.5898 -1.2385 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5517 0.6540 -1.8564 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8754 -0.8838 -2.4002 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6756 1.0828 -3.0996 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9559 0.4622 -2.8766 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2530 1.4782 -2.2577 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3480 -0.1796 -1.2271 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3626 -1.3469 -2.1395 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7670 -1.5530 -0.2372 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3424 -1.8110 -0.6474 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4527 -0.8427 2.8085 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8035 -2.5241 2.4417 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4635 1.6997 1.7160 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7385 2.0142 -0.0070 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3856 0.5259 0.7438 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1021 -0.5835 1.8335 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8741 0.9447 2.4842 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3289 2.2266 1.0433 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7493 0.5698 3.2255 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1647 3.0129 -1.1603 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9824 0.5577 2.6447 H 0 0 0 0 0 0 0 0 0 0 0 0 5.3858 2.2435 -0.3912 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7338 -2.1491 -1.5525 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1107 -0.6457 0.0511 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 6 13 14 1 0 12 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 19 21 1 6 16 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 2 0 27 28 1 0 28 29 2 0 28 30 1 0 30 31 1 0 25 32 1 0 32 33 1 1 32 34 1 0 34 35 1 0 35 36 1 0 22 37 1 1 11 38 1 0 5 39 1 0 4 40 1 0 3 41 1 0 7 2 1 0 20 9 1 0 32 22 1 0 19 12 1 0 31 26 1 0 35 15 1 0 1 42 1 0 1 43 1 0 1 44 1 0 2 45 1 0 3 46 1 6 4 47 1 0 5 48 1 6 6 49 1 0 9 50 1 6 10 51 1 0 10 52 1 0 11 53 1 1 13 54 1 0 13 55 1 0 14 56 1 0 15 57 1 1 16 58 1 6 17 59 1 0 17 60 1 0 18 61 1 0 18 62 1 0 20 63 1 0 20 64 1 0 21 65 1 0 23 66 1 0 23 67 1 0 24 68 1 0 24 69 1 0 25 70 1 6 27 71 1 0 31 72 1 0 31 73 1 0 33 74 1 0 33 75 1 0 33 76 1 0 34 77 1 0 34 78 1 0 35 79 1 6 36 80 1 0 37 81 1 0 38 82 1 0 39 83 1 0 40 84 1 0 41 85 1 0 M END

Standard InCHIKey	LPMXVESGRSUGHW-PCZRPPSHSA-N
Standard InCHI	InChI=1S/C29H44O12/c1-13-22(34)23(35)24(36)25(40-13)41-15-8-19(32)28(12-30)21-17(3-5-27(28,37)9-15)29(38)6-4-16(14-7-20(33)39-11-14)26(29,2)10-18(21)31/h7,13,15-19,21-25,30-32,34-38H,3-6,8-12H2,1-2H3/t13?,15-,16+,17+,18+,19+,21+,22-,23?,24-,25?,26+,27-,28+,29-/m0/s1
SMILES	CC1[C@@H](C([C@@H](C(O1)O[C@H]1C[C@H]([C@]2(CO)[C@@H]3[C@@H](CC[C@@]2(C1)O)[C@]1(CC[C@H](C2=CC(=O)OC2)[C@@]1(C)C[C@H]3O)O)O)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
NPO16145	Apocynum venetum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO16145	Apocynum venetum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO16145	Apocynum venetum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO16145	Apocynum venetum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO16145	Apocynum venetum	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]

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

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

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 NPC196839 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	16367
0.1-0.2	29132
0.2-0.3	4056
0.3-0.4	137
0.4-0.5	104
0.5-0.6	34
0.6-0.7	23
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	NPC83287
0.6867	Remote Similarity	NPC157376
0.6867	Remote Similarity	NPC142066
0.6867	Remote Similarity	NPC603972
0.6627	Remote Similarity	NPC99728
0.6627	Remote Similarity	NPC87250
0.6627	Remote Similarity	NPC244402
0.6627	Remote Similarity	NPC50305
0.6471	Remote Similarity	NPC17896
0.6471	Remote Similarity	NPC469755
0.6471	Remote Similarity	NPC284406
0.6471	Remote Similarity	NPC197707
0.6471	Remote Similarity	NPC251866
0.6304	Remote Similarity	NPC264336
0.618	Remote Similarity	NPC471354
0.618	Remote Similarity	NPC27507
0.6163	Remote Similarity	NPC196429
0.6163	Remote Similarity	NPC309034
0.6136	Remote Similarity	NPC77319
0.6136	Remote Similarity	NPC471351
0.6136	Remote Similarity	NPC471355
0.6064	Remote Similarity	NPC59288
0.6023	Remote Similarity	NPC76572
0.6023	Remote Similarity	NPC193382
0.5977	Remote Similarity	NPC84987
0.5889	Remote Similarity	NPC9499
0.5889	Remote Similarity	NPC471360
0.5889	Remote Similarity	NPC469751
0.5889	Remote Similarity	NPC471361
0.5889	Remote Similarity	NPC86159
0.5889	Remote Similarity	NPC469752
0.5889	Remote Similarity	NPC469754
0.5889	Remote Similarity	NPC70542
0.5862	Remote Similarity	NPC99620
0.573	Remote Similarity	NPC469750
0.5543	Remote Similarity	NPC471353
0.5521	Remote Similarity	NPC240070
0.551	Remote Similarity	NPC469749
0.5393	Remote Similarity	NPC158344
0.5385	Remote Similarity	NPC5311
0.5385	Remote Similarity	NPC77299
0.5385	Remote Similarity	NPC480906
0.5361	Remote Similarity	NPC32793
0.5361	Remote Similarity	NPC116075
0.5306	Remote Similarity	NPC475629
0.5275	Remote Similarity	NPC219085
0.5258	Remote Similarity	NPC27363
0.5222	Remote Similarity	NPC474418
0.5217	Remote Similarity	NPC480915
0.5213	Remote Similarity	NPC179412
0.5213	Remote Similarity	NPC471356
0.5204	Remote Similarity	NPC475556
0.5204	Remote Similarity	NPC471357
0.5204	Remote Similarity	NPC469757
0.5204	Remote Similarity	NPC117702
0.5204	Remote Similarity	NPC311706
0.5161	Remote Similarity	NPC480914
0.5106	Remote Similarity	NPC146456

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC196839 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6226
0.1-0.2	2827
0.2-0.3	82
0.3-0.4	7
0.4-0.5	5
0.5-0.6	0
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	2

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD7327	Approved
1.0	High Similarity	NPD7328	Phase 4
0.6471	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