NPASS Compound

Natural Product: NPC73516

Natural Product ID	NPC73516
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	CIQDSODCPIIBBH-OWQLDQOQSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	5318966
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000258] Steroids and steroid derivatives [CHEMONTID:0002031] Stigmastanes 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 84 87 0 0 0 0 0 0 0 0999 V2000 -7.6234 1.0952 0.5217 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2028 0.9855 -0.0181 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.6305 -0.3857 0.1085 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2585 -0.5319 -0.4186 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2379 0.2933 0.2428 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8308 0.0486 -0.3727 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.8115 0.7873 -1.6588 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8176 0.4857 0.6243 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8317 1.9309 1.0099 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6505 2.3845 0.9845 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3016 1.4270 0.0413 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7394 1.1708 0.2629 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4143 2.0502 0.9545 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8279 1.8645 1.2113 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4419 2.6358 1.9917 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5594 0.7740 0.5633 C 0 0 2 0 0 0 0 0 0 0 0 0 6.3269 1.3360 -0.6059 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3592 0.3681 -1.0627 C 0 0 2 0 0 0 0 0 0 0 0 0 6.8271 -1.0102 -1.0566 C 0 0 2 0 0 0 0 0 0 0 0 0 5.3526 -1.1835 -0.9679 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7103 -0.4094 0.1694 C 0 0 1 0 0 0 0 0 0 0 0 0 4.7033 -1.3409 1.3626 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3429 -0.0121 -0.3028 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4638 -1.2381 -0.2985 C 0 0 0 0 0 0 0 0 0 0 0 0 0.9900 -0.8724 -0.5340 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5894 0.1405 0.4609 C 0 0 2 0 0 0 0 0 0 0 0 0 1.1575 -0.1635 1.8615 C 0 0 0 0 0 0 0 0 0 0 0 0 7.5106 -1.7349 -0.0549 O 0 0 0 0 0 0 0 0 0 0 0 0 8.5722 0.5021 -0.3820 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1257 1.7257 -1.2981 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8138 -1.3131 -0.6056 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4582 1.6045 0.4764 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5909 -1.4038 -0.4856 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0225 -2.8076 -0.3833 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9766 -1.1299 -1.8938 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7361 -1.4092 0.3077 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.8495 2.1682 0.7244 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.3861 0.7369 -0.1716 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.6523 0.5617 1.4808 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6192 1.7174 0.5712 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1575 1.3738 -1.0706 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6521 -0.6203 1.2247 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9146 -1.6025 -0.4385 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2549 -0.2690 -1.5272 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0852 -0.1725 1.2887 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5850 1.8721 -1.5574 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.7475 0.7614 -2.2511 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0312 0.4141 -2.3881 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1499 -0.0470 1.5958 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4224 2.5936 0.3487 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1528 2.1408 2.0479 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7212 3.4366 0.6613 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0974 2.2899 1.9740 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8991 2.9628 1.3539 H 0 0 0 0 0 0 0 0 0 0 0 0 6.3538 0.4405 1.2991 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6771 1.6095 -1.4574 H 0 0 0 0 0 0 0 0 0 0 0 0 6.8464 2.2518 -0.2423 H 0 0 0 0 0 0 0 0 0 0 0 0 7.6128 0.6698 -2.1255 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1485 -1.5153 -2.0125 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8621 -0.9081 -1.9226 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1270 -2.2522 -0.7997 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5026 -2.3939 1.0929 H 0 0 0 0 0 0 0 0 0 0 0 0 3.9028 -1.0191 2.0544 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6457 -1.2407 1.9604 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5092 0.2428 -1.4088 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6030 -1.9025 0.5657 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7473 -1.8453 -1.1895 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4424 -1.8192 -0.5421 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0404 -0.3837 -1.5529 H 0 0 0 0 0 0 0 0 0 0 0 0 2.0220 0.4382 2.1186 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3741 -1.2189 2.0120 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3873 0.0835 2.6558 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2387 -2.6851 -0.0520 H 0 0 0 0 0 0 0 0 0 0 0 0 8.6018 -0.1196 0.4131 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9452 1.6093 -1.8360 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9226 -1.8594 0.1947 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4286 1.8824 1.4273 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8911 -3.4969 -0.4279 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5376 -2.9897 0.5961 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3761 -3.0682 -1.2420 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0695 -0.8530 -1.9635 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3535 -0.3692 -2.3974 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.8932 -2.0602 -2.4905 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.2990 -2.2094 0.1613 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 2 0 13 14 1 0 14 15 2 0 14 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 1 21 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 1 19 28 1 0 18 29 1 0 11 30 1 0 6 31 1 6 5 32 1 0 3 33 1 0 33 34 1 0 33 35 1 0 33 36 1 0 26 8 1 0 26 11 1 0 23 12 1 0 21 16 1 0 1 37 1 0 1 38 1 0 1 39 1 0 2 40 1 0 2 41 1 0 3 42 1 0 4 43 1 0 4 44 1 0 5 45 1 0 7 46 1 0 7 47 1 0 7 48 1 0 8 49 1 0 9 50 1 0 9 51 1 0 10 52 1 0 10 53 1 0 13 54 1 0 16 55 1 1 17 56 1 0 17 57 1 0 18 58 1 6 19 59 1 6 20 60 1 0 20 61 1 0 22 62 1 0 22 63 1 0 22 64 1 0 23 65 1 0 24 66 1 0 24 67 1 0 25 68 1 0 25 69 1 0 27 70 1 0 27 71 1 0 27 72 1 0 28 73 1 0 29 74 1 0 30 75 1 0 31 76 1 0 32 77 1 0 34 78 1 0 34 79 1 0 34 80 1 0 35 81 1 0 35 82 1 0 35 83 1 0 36 84 1 0 M END

Standard InCHIKey	CIQDSODCPIIBBH-OWQLDQOQSA-N
Standard InCHI	InChI=1S/C29H48O7/c1-7-16(25(2,3)34)12-24(33)28(6,35)23-9-11-29(36)18-13-20(30)19-14-21(31)22(32)15-26(19,4)17(18)8-10-27(23,29)5/h13,16-17,19,21-24,31-36H,7-12,14-15H2,1-6H3/t16?,17?,19-,21+,22-,23?,24?,26+,27+,28+,29?/m0/s1
SMILES	CCC(CC([C@@](C)(C1CCC2(C3=CC(=O)[C@@H]4C[C@H]([C@H](C[C@]4(C)C3CC[C@]12C)O)O)O)O)O)C(C)(C)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
NPO27558	Podocarpus macrophyllus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27558	Podocarpus macrophyllus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13426	Lemmaphyllum microphyllum	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO13426	Lemmaphyllum microphyllum	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27558	Podocarpus macrophyllus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27558	Podocarpus macrophyllus	Species	Podocarpaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO13426	Lemmaphyllum microphyllum	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27558	Podocarpus macrophyllus	Species	Podocarpaceae	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

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 NPC73516 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	19740
0.1-0.2	27253
0.2-0.3	2798
0.3-0.4	13
0.4-0.5	6
0.5-0.6	10
0.6-0.7	15
0.7-0.8	0
0.8-0.85	14
0.85-0.9	1
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC296945
0.8793	High Similarity	NPC214264
0.8475	Intermediate Similarity	NPC475060
0.8475	Intermediate Similarity	NPC85829
0.8475	Intermediate Similarity	NPC50692
0.8475	Intermediate Similarity	NPC260268
0.8475	Intermediate Similarity	NPC152695
0.8475	Intermediate Similarity	NPC319077
0.8475	Intermediate Similarity	NPC97202
0.8475	Intermediate Similarity	NPC601752
0.8226	Intermediate Similarity	NPC476027
0.8167	Intermediate Similarity	NPC48733
0.8167	Intermediate Similarity	NPC171137
0.8167	Intermediate Similarity	NPC83744
0.8033	Intermediate Similarity	NPC220229
0.8033	Intermediate Similarity	NPC601682
0.7778	Intermediate Similarity	NPC202167
0.7778	Intermediate Similarity	NPC49958
0.7692	Intermediate Similarity	NPC49492
0.7692	Intermediate Similarity	NPC266728
0.7313	Intermediate Similarity	NPC600136
0.7143	Intermediate Similarity	NPC302607
0.7015	Intermediate Similarity	NPC207251
0.6866	Remote Similarity	NPC317210
0.6719	Remote Similarity	NPC150531
0.662	Remote Similarity	NPC109973
0.6615	Remote Similarity	NPC600374
0.6515	Remote Similarity	NPC76084
0.6364	Remote Similarity	NPC11710
0.6364	Remote Similarity	NPC204833
0.6364	Remote Similarity	NPC209502
0.6364	Remote Similarity	NPC477915
0.6364	Remote Similarity	NPC610677
0.6301	Remote Similarity	NPC475041
0.6269	Remote Similarity	NPC329417
0.6269	Remote Similarity	NPC149047
0.6119	Remote Similarity	NPC217201
0.6119	Remote Similarity	NPC451956
0.5972	Remote Similarity	NPC250109
0.5938	Remote Similarity	NPC603391
0.5735	Remote Similarity	NPC108721
0.5735	Remote Similarity	NPC73300
0.5658	Remote Similarity	NPC600372
0.5556	Remote Similarity	NPC28532
0.5541	Remote Similarity	NPC606024
0.5405	Remote Similarity	NPC222688
0.5333	Remote Similarity	NPC326542
0.5286	Remote Similarity	NPC154072

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC73516 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6766
0.1-0.2	2250
0.2-0.3	134
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