NPASS Compound

Natural Product: NPC602967

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 78 82 0 0 0 0 0 0 0 0999 V2000 8.1472 5.5157 0.0729 C 0 0 0 0 0 0 0 0 0 0 0 0 8.6122 4.4104 0.7993 O 0 0 0 0 0 0 0 0 0 0 0 0 7.7964 3.2946 0.9346 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2266 2.2027 1.6386 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3926 1.0784 1.7694 C 0 0 0 0 0 0 0 0 0 0 0 0 6.1565 1.0355 1.2140 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2818 -0.1131 1.3367 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6830 -1.2186 2.0321 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8638 -2.3428 2.1692 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1894 -3.3657 2.7916 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6285 -2.2831 1.5680 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7438 -3.3280 1.6383 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1133 -4.4887 2.3443 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5150 -3.2862 1.0484 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6743 -4.3887 1.1656 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7026 -5.4372 0.2188 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1308 -2.1398 0.3421 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1020 -2.1190 -0.2398 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6812 -1.0887 -0.9792 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.8282 -0.6449 -0.3449 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9629 -1.2658 -0.8036 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.0727 -1.2901 0.2254 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5037 -0.0837 0.6584 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.0196 0.7757 -0.2731 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1820 1.8444 -0.3638 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4691 2.9687 0.3322 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.8144 4.1558 -0.5667 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4665 2.8235 1.4498 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.9280 2.1004 2.4868 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.7189 2.1322 0.9853 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.5779 3.1020 0.4722 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.4659 1.1089 -0.0776 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.0045 1.5260 -1.2946 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6469 -2.7169 -1.0913 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.8772 -3.3523 -1.2693 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7653 -2.8678 -2.3017 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9631 -3.9942 -2.1654 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9188 -1.6245 -2.3776 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5037 -0.7111 -3.2272 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0270 -1.1074 0.2829 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2908 -1.1396 0.8847 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0809 -0.1120 0.7785 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7294 2.1578 0.4974 C 0 0 0 0 0 0 0 0 0 0 0 0 6.5494 3.2584 0.3711 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0154 6.2054 -0.0758 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3161 6.0520 0.5790 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8509 5.1841 -0.9574 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1982 2.2005 2.0916 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8003 0.2637 2.3352 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6478 -1.3070 2.5207 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5628 -5.2206 1.8170 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3300 -6.2481 0.6587 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1732 -5.0636 -0.7257 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3322 -5.7693 0.0478 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0063 -0.1839 -1.0724 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2749 -0.7823 -1.7476 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8894 -1.9649 -0.1063 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6251 -1.8202 1.1205 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9635 0.2420 -1.2700 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.5085 3.2897 0.8424 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8325 4.0661 -0.9943 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7918 5.1076 0.0025 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0190 4.2360 -1.3364 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7040 3.8733 1.7899 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.4122 2.2353 3.3405 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2449 1.6947 1.8657 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.1891 2.7343 -0.2162 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0259 0.1961 0.2112 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3605 1.4593 -2.0404 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1609 -3.1829 -0.2298 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.3788 -3.0319 -2.0437 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4309 -2.9823 -3.1817 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4544 -4.7936 -1.8977 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0441 -1.9240 -2.8488 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1421 0.2033 -3.0990 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7816 -0.1880 -0.2544 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7488 2.1016 0.0672 H 0 0 0 0 0 0 0 0 0 0 0 0 6.2148 4.1364 -0.1898 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 2 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 9 11 1 0 11 12 2 0 12 13 1 0 12 14 1 0 14 15 1 0 15 16 1 0 14 17 2 0 17 18 1 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 1 0 22 23 1 0 23 24 1 0 24 25 1 0 25 26 1 0 26 27 1 0 26 28 1 0 28 29 1 0 28 30 1 0 30 31 1 0 30 32 1 0 32 33 1 0 21 34 1 0 34 35 1 0 34 36 1 0 36 37 1 0 36 38 1 0 38 39 1 0 17 40 1 0 40 41 2 0 41 42 1 0 6 43 1 0 43 44 2 0 44 3 1 0 42 7 1 0 41 11 1 0 38 19 1 0 32 24 1 0 1 45 1 0 1 46 1 0 1 47 1 0 4 48 1 0 5 49 1 0 8 50 1 0 13 51 1 0 16 52 1 0 16 53 1 0 16 54 1 0 19 55 1 6 21 56 1 6 22 57 1 0 22 58 1 0 24 59 1 6 26 60 1 1 27 61 1 0 27 62 1 0 27 63 1 0 28 64 1 1 29 65 1 0 30 66 1 1 31 67 1 0 32 68 1 1 33 69 1 0 34 70 1 1 35 71 1 0 36 72 1 6 37 73 1 0 38 74 1 6 39 75 1 0 40 76 1 0 43 77 1 0 44 78 1 0 M END

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

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 NPC602967 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	14819
0.1-0.2	30424
0.2-0.3	3563
0.3-0.4	686
0.4-0.5	249
0.5-0.6	87
0.6-0.7	20
0.7-0.8	1
0.8-0.85	5
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	NPC204693
0.8395	Intermediate Similarity	NPC211594
0.8256	Intermediate Similarity	NPC483707
0.8214	Intermediate Similarity	NPC22062
0.8214	Intermediate Similarity	NPC473634
0.8214	Intermediate Similarity	NPC138811
0.7253	Intermediate Similarity	NPC209296
0.7229	Intermediate Similarity	NPC186807
0.7079	Intermediate Similarity	NPC44931
0.6932	Remote Similarity	NPC172807
0.6897	Remote Similarity	NPC99957
0.6882	Remote Similarity	NPC473623
0.6813	Remote Similarity	NPC210073
0.6809	Remote Similarity	NPC488089
0.6786	Remote Similarity	NPC58053
0.6667	Remote Similarity	NPC254540
0.6667	Remote Similarity	NPC475366
0.6633	Remote Similarity	NPC11468
0.6275	Remote Similarity	NPC473644
0.625	Remote Similarity	NPC105025
0.6237	Remote Similarity	NPC295613
0.6237	Remote Similarity	NPC187379
0.6237	Remote Similarity	NPC473657
0.6214	Remote Similarity	NPC311850
0.6146	Remote Similarity	NPC46202
0.6111	Remote Similarity	NPC609451
0.6038	Remote Similarity	NPC68592
0.6	Remote Similarity	NPC101636
0.6	Remote Similarity	NPC201292
0.5938	Remote Similarity	NPC475155
0.59	Remote Similarity	NPC475382
0.59	Remote Similarity	NPC473073
0.5889	Remote Similarity	NPC181712
0.587	Remote Similarity	NPC605067
0.5856	Remote Similarity	NPC262222
0.5833	Remote Similarity	NPC67105
0.5806	Remote Similarity	NPC602805
0.5778	Remote Similarity	NPC93337
0.5778	Remote Similarity	NPC95090
0.5778	Remote Similarity	NPC27408
0.5773	Remote Similarity	NPC473512
0.5773	Remote Similarity	NPC233994
0.5773	Remote Similarity	NPC129827
0.5769	Remote Similarity	NPC145379
0.5758	Remote Similarity	NPC470443
0.5741	Remote Similarity	NPC488086
0.5714	Remote Similarity	NPC473571
0.5714	Remote Similarity	NPC110941
0.5714	Remote Similarity	NPC186816
0.5701	Remote Similarity	NPC488087
0.57	Remote Similarity	NPC473327
0.567	Remote Similarity	NPC227508
0.5657	Remote Similarity	NPC284277
0.5657	Remote Similarity	NPC126784
0.5657	Remote Similarity	NPC241423
0.5657	Remote Similarity	NPC475497
0.5631	Remote Similarity	NPC135358
0.56	Remote Similarity	NPC211532
0.56	Remote Similarity	NPC488364
0.5556	Remote Similarity	NPC257566
0.5556	Remote Similarity	NPC331652
0.5556	Remote Similarity	NPC488083
0.5545	Remote Similarity	NPC198199
0.5543	Remote Similarity	NPC45638
0.5534	Remote Similarity	NPC298171
0.551	Remote Similarity	NPC15358
0.5474	Remote Similarity	NPC607707
0.5446	Remote Similarity	NPC65711
0.5405	Remote Similarity	NPC298666
0.5398	Remote Similarity	NPC120952
0.5385	Remote Similarity	NPC473043
0.5385	Remote Similarity	NPC114740
0.5354	Remote Similarity	NPC173582
0.5354	Remote Similarity	NPC265885
0.5354	Remote Similarity	NPC181465
0.5354	Remote Similarity	NPC215710
0.5354	Remote Similarity	NPC473438
0.5354	Remote Similarity	NPC253788
0.5347	Remote Similarity	NPC64051
0.5326	Remote Similarity	NPC19709
0.53	Remote Similarity	NPC203259
0.53	Remote Similarity	NPC65563
0.53	Remote Similarity	NPC33054
0.53	Remote Similarity	NPC470949
0.53	Remote Similarity	NPC176740
0.53	Remote Similarity	NPC471725
0.53	Remote Similarity	NPC303913
0.53	Remote Similarity	NPC134532
0.53	Remote Similarity	NPC602582
0.5294	Remote Similarity	NPC469622
0.5288	Remote Similarity	NPC476472
0.5288	Remote Similarity	NPC294815
0.5288	Remote Similarity	NPC16194
0.5288	Remote Similarity	NPC477629
0.5283	Remote Similarity	NPC244875
0.5243	Remote Similarity	NPC229409
0.5213	Remote Similarity	NPC27640
0.5208	Remote Similarity	NPC243930
0.5208	Remote Similarity	NPC181616
0.52	Remote Similarity	NPC39834
0.5192	Remote Similarity	NPC142142
0.5192	Remote Similarity	NPC270675
0.5192	Remote Similarity	NPC195685
0.5161	Remote Similarity	NPC143851
0.5158	Remote Similarity	NPC27942
0.5146	Remote Similarity	NPC483414
0.5146	Remote Similarity	NPC483415
0.514	Remote Similarity	NPC475261
0.5138	Remote Similarity	NPC472993
0.5096	Remote Similarity	NPC483416
0.5096	Remote Similarity	NPC257714
0.5094	Remote Similarity	NPC287889
0.5089	Remote Similarity	NPC488088
0.5052	Remote Similarity	NPC22832
0.5052	Remote Similarity	NPC21666
0.5047	Remote Similarity	NPC472994

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC602967 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4441
0.1-0.2	4601
0.2-0.3	95
0.3-0.4	6
0.4-0.5	2
0.5-0.6	3
0.6-0.7	1
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
0.7253	Intermediate Similarity	NPD7054	Phase 4
0.63	Remote Similarity	NPD7472	Pre-clinical
0.5673	Remote Similarity	NPD7808	Phase 3
0.5437	Remote Similarity	NPD7251	Phase 2
0.53	Remote Similarity	NPD6797	Phase 2

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