NPASS Compound

Natural Product: NPC610937

Natural Product ID	NPC610937
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	PSVZSZBQAZPKNI-IEGIENCHSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL5207388
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 81 85 0 0 0 0 0 0 0 0999 V2000 2.9033 -3.0361 0.9167 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2003 -1.5332 0.6359 C 0 0 2 0 0 0 0 0 0 0 0 0 2.7788 -1.1582 -0.7142 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4158 -0.6043 -0.8962 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5376 -1.3260 -1.5335 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8663 -0.8935 -1.7931 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2441 -0.0748 -0.6007 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.7387 0.1405 -0.4848 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.3388 1.0834 -1.4489 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3575 -1.2360 -0.8223 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.8036 -1.3171 -0.3671 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0525 -0.8704 1.0175 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.4122 -0.7509 1.2207 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3993 0.4169 1.4069 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2057 1.6259 1.0421 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3641 0.3827 2.9474 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9865 0.4322 0.9597 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.2241 1.6653 1.3303 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7445 1.3946 1.1865 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3710 1.0765 -0.2838 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6329 2.3489 -1.0257 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0733 0.7319 -0.4326 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7215 1.1829 0.8611 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8230 1.6119 -1.4819 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9518 0.9209 -2.1487 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6501 -0.2240 -1.5212 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1915 -1.0324 -2.7476 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9165 0.2154 -0.8730 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5283 -0.9741 -0.1920 C 0 0 0 0 0 0 0 0 0 0 0 0 4.6639 -1.3751 0.9454 C 0 0 1 0 0 0 0 0 0 0 0 0 4.8967 -0.4580 2.0882 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5932 0.5528 1.9353 O 0 0 0 0 0 0 0 0 0 0 0 0 4.3438 -0.7167 3.3301 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4132 -3.6399 0.1658 H 0 0 0 0 0 0 0 0 0 0 0 0 1.8135 -3.1580 0.9445 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3413 -3.2313 1.9169 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6449 -1.0916 1.4899 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8298 -2.1498 -1.2780 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7886 -2.3384 -1.9372 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9563 -0.3414 -2.7512 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4984 -1.7836 -1.8462 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0502 -0.8070 0.2597 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8218 1.0010 -2.4254 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3863 0.7204 -1.6869 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5135 2.1160 -1.1031 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4378 -1.2874 -1.9343 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8251 -2.0566 -0.3502 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5079 -0.8805 -1.1301 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0460 -2.4221 -0.4079 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6879 -1.6764 1.7137 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.9465 -1.1221 0.4717 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7900 1.4749 0.1038 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9974 1.8165 1.8267 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6331 2.5479 0.9718 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3048 -0.0671 3.2990 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1455 1.3645 3.3704 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5586 -0.3723 3.1856 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4754 -0.4105 1.5241 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5938 2.5978 0.9357 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3638 1.7689 2.4604 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2368 2.2536 1.5892 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6218 0.4371 1.7877 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2678 3.0296 -0.9158 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4019 3.0147 -0.5455 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8277 2.2641 -2.0902 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2682 0.8497 1.7768 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5526 2.3143 0.8337 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8098 1.1341 0.8799 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2013 2.5428 -1.0151 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1190 1.8981 -2.3035 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6682 0.6596 -3.2254 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7564 1.7018 -2.3509 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3666 -1.0988 -3.4951 H 0 0 0 0 0 0 0 0 0 0 0 0 4.3846 -2.0714 -2.4080 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0583 -0.5283 -3.1729 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6091 0.5245 -1.7271 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8222 1.0494 -0.1711 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7313 -1.8118 -0.8892 H 0 0 0 0 0 0 0 0 0 0 0 0 6.4994 -0.6082 0.2550 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1207 -2.3567 1.3145 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1144 0.0276 3.9967 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 2 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 6 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 12 14 1 0 14 15 1 0 14 16 1 0 14 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 6 20 22 1 0 22 23 1 1 22 24 1 0 24 25 1 0 25 26 1 0 26 27 1 6 26 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 2 0 31 33 1 0 30 2 1 0 26 3 1 0 22 4 1 0 20 7 1 0 17 8 1 0 1 34 1 0 1 35 1 0 1 36 1 0 2 37 1 1 3 38 1 6 5 39 1 0 6 40 1 0 6 41 1 0 7 42 1 1 9 43 1 0 9 44 1 0 9 45 1 0 10 46 1 0 10 47 1 0 11 48 1 0 11 49 1 0 12 50 1 1 13 51 1 0 15 52 1 0 15 53 1 0 15 54 1 0 16 55 1 0 16 56 1 0 16 57 1 0 17 58 1 1 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 23 66 1 0 23 67 1 0 23 68 1 0 24 69 1 0 24 70 1 0 25 71 1 0 25 72 1 0 27 73 1 0 27 74 1 0 27 75 1 0 28 76 1 0 28 77 1 0 29 78 1 0 29 79 1 0 30 80 1 1 33 81 1 0 M END

Standard InCHIKey	PSVZSZBQAZPKNI-IEGIENCHSA-N
Standard InCHI	InChI=1S/C30H48O3/c1-18-19(25(32)33)10-13-27(4)16-17-29(6)20(24(18)27)8-9-22-28(5)14-12-23(31)26(2,3)21(28)11-15-30(22,29)7/h8,18-19,21-24,31H,9-17H2,1-7H3,(H,32,33)/t18-,19+,21-,22+,23-,24-,27+,28-,29+,30+/m0/s1
SMILES	C[C@@H]1[C@H]2C3=CC[C@@H]4[C@@]5(C)CC[C@H](O)C(C)(C)[C@@H]5CC[C@@]4(C)[C@]3(C)CC[C@@]2(C)CC[C@H]1C(=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
NPO57882	Tripterygium wilfordii Hook f.	Genus	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]

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
Inhibition	1

Activity Type	# Activity
Individual protein	1

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT5212	Individual protein	Sentrin-specific protease 1	Homo sapiens	Inhibition	=	69.2	%	PMID[35500202]

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 NPC610937 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	22271
0.1-0.2	23130
0.2-0.3	3292
0.3-0.4	894
0.4-0.5	193
0.5-0.6	49
0.6-0.7	17
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	Natural Product ID
0.7778	Intermediate Similarity	NPC18872
0.7778	Intermediate Similarity	NPC290614
0.6833	Remote Similarity	NPC27765
0.6833	Remote Similarity	NPC122418
0.6833	Remote Similarity	NPC491014
0.6567	Remote Similarity	NPC112866
0.6324	Remote Similarity	NPC171203
0.6324	Remote Similarity	NPC307426
0.6324	Remote Similarity	NPC98442
0.6324	Remote Similarity	NPC242468
0.6176	Remote Similarity	NPC187722
0.6087	Remote Similarity	NPC7260
0.6087	Remote Similarity	NPC210037
0.6087	Remote Similarity	NPC120968
0.6087	Remote Similarity	NPC227467
0.6087	Remote Similarity	NPC273621
0.6032	Remote Similarity	NPC290598
0.6032	Remote Similarity	NPC30590
0.6029	Remote Similarity	NPC477872
0.5942	Remote Similarity	NPC480946
0.5942	Remote Similarity	NPC130577
0.5942	Remote Similarity	NPC142415
0.5942	Remote Similarity	NPC102683
0.5857	Remote Similarity	NPC182797
0.5857	Remote Similarity	NPC51700
0.5857	Remote Similarity	NPC88716
0.5857	Remote Similarity	NPC68160
0.5857	Remote Similarity	NPC52169
0.5857	Remote Similarity	NPC488562
0.5857	Remote Similarity	NPC606443
0.5821	Remote Similarity	NPC95594
0.5797	Remote Similarity	NPC477579
0.5753	Remote Similarity	NPC105189
0.5694	Remote Similarity	NPC202728
0.5694	Remote Similarity	NPC158059
0.5694	Remote Similarity	NPC293564
0.5672	Remote Similarity	NPC235341
0.5672	Remote Similarity	NPC40394
0.5652	Remote Similarity	NPC40552
0.5522	Remote Similarity	NPC101475
0.5493	Remote Similarity	NPC274330
0.5493	Remote Similarity	NPC86372
0.5493	Remote Similarity	NPC198664
0.5479	Remote Similarity	NPC228784
0.5479	Remote Similarity	NPC324341
0.5479	Remote Similarity	NPC601810
0.5429	Remote Similarity	NPC246708
0.5417	Remote Similarity	NPC142361
0.5417	Remote Similarity	NPC474684
0.5405	Remote Similarity	NPC263393
0.5362	Remote Similarity	NPC470588
0.5312	Remote Similarity	NPC212733
0.5303	Remote Similarity	NPC120098
0.5294	Remote Similarity	NPC132478
0.5205	Remote Similarity	NPC229281
0.5205	Remote Similarity	NPC195019
0.5135	Remote Similarity	NPC470375
0.5135	Remote Similarity	NPC470376
0.5072	Remote Similarity	NPC311078
0.5072	Remote Similarity	NPC34177
0.5072	Remote Similarity	NPC196753
0.507	Remote Similarity	NPC480950
0.5068	Remote Similarity	NPC2539
0.5067	Remote Similarity	NPC49776
0.5067	Remote Similarity	NPC63118
0.5067	Remote Similarity	NPC474436
0.5067	Remote Similarity	NPC29765
0.5062	Remote Similarity	NPC603645

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC610937 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6296
0.1-0.2	2781
0.2-0.3	68
0.3-0.4	2
0.4-0.5	3
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