NPASS Compound

Natural Product: NPC607951

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 79 83 0 0 0 0 0 0 0 0999 V2000 -3.6268 -1.2980 -3.2018 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8942 -0.3563 -2.3084 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1171 1.0416 -2.7625 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9830 -0.6373 -0.8488 C 0 0 2 0 0 0 0 0 0 0 0 0 -5.2976 -0.0659 -0.3684 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9949 0.9490 0.6958 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6380 0.5295 1.1907 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.7400 -0.6553 2.0718 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3622 -0.6507 3.2666 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2753 -1.8705 1.6081 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8393 1.5846 1.8318 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3655 1.4889 1.7402 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7860 0.6607 0.6638 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.6461 1.5476 -0.5720 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7026 -0.4878 0.2234 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.0974 -1.3418 -0.8237 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2889 -1.8336 -0.4093 C 0 0 0 0 0 0 0 0 0 0 0 0 1.1069 -0.6453 -0.0918 C 0 0 2 0 0 0 0 0 0 0 0 0 2.6039 -0.8713 -0.0694 C 0 0 1 0 0 0 0 0 0 0 0 0 3.0777 -1.6492 1.1218 C 0 0 0 0 0 0 0 0 0 0 0 0 2.9758 -1.6950 -1.2886 C 0 0 0 0 0 0 0 0 0 0 0 0 4.4746 -1.7983 -1.4537 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2213 -0.6619 -0.9074 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4305 -0.7922 -0.7883 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5972 0.6104 -0.5008 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4595 1.1951 0.6271 C 0 0 0 0 0 0 0 0 0 0 0 0 4.8164 1.5731 -1.6808 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1780 0.5235 -0.1230 C 0 0 2 0 0 0 0 0 0 0 0 0 2.8573 1.2017 1.1886 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4151 1.2660 1.5143 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5849 0.1010 1.0908 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3382 -0.7861 2.2899 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9675 0.1767 -0.1465 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.5712 -1.0508 -4.2537 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4687 -2.3135 -2.8331 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2115 1.4643 -3.2725 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9231 1.0936 -3.5425 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.4658 1.6983 -1.9410 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9029 -1.7268 -0.6948 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.8710 0.4380 -1.1690 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9000 -0.9163 0.0024 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.0413 1.9868 0.3702 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.7184 0.7651 1.5354 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9039 -2.7269 2.0182 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.2310 2.5824 1.4696 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1083 1.5935 2.9316 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9829 2.5478 1.5978 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8969 1.2086 2.7309 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3179 2.4543 -0.4727 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9569 1.0445 -1.4950 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3503 1.9549 -0.7262 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.9296 -1.1749 1.0920 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0933 -0.9531 -1.8403 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7195 -2.2858 -0.8657 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2478 -2.6309 0.3183 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6896 -2.3014 -1.3586 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9541 0.0371 -0.9871 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1644 -1.8326 0.9856 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9517 -1.1680 2.0837 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6088 -2.6660 1.0438 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6440 -2.7476 -1.0397 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4664 -1.3621 -2.2022 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7086 -1.9590 -2.5456 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8918 -2.7250 -0.9601 H 0 0 0 0 0 0 0 0 0 0 0 0 5.4391 0.5875 1.5291 H 0 0 0 0 0 0 0 0 0 0 0 0 5.2529 2.2736 0.7782 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5197 1.1584 0.2386 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5431 2.6088 -1.3924 H 0 0 0 0 0 0 0 0 0 0 0 0 5.8636 1.5372 -2.0126 H 0 0 0 0 0 0 0 0 0 0 0 0 4.1451 1.2975 -2.5349 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5805 1.0902 -0.8991 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2358 2.2623 1.0709 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4752 0.7995 2.0320 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3514 1.3685 2.6430 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9888 2.2579 1.1737 H 0 0 0 0 0 0 0 0 0 0 0 0 0.6510 -1.8325 2.1432 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6886 -0.8072 2.6508 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9496 -0.4276 3.1727 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8632 1.1444 -0.6783 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 2 0 2 3 1 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 1 8 9 2 0 8 10 1 0 7 11 1 0 11 12 1 0 12 13 1 0 13 14 1 6 13 15 1 0 15 16 1 0 16 17 1 0 17 18 1 0 18 19 1 0 19 20 1 1 19 21 1 0 21 22 1 0 22 23 1 0 23 24 2 0 23 25 1 0 25 26 1 0 25 27 1 0 25 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 31 32 1 1 15 33 1 0 33 4 1 0 33 7 1 0 31 13 1 0 31 18 1 0 28 19 1 0 1 34 1 0 1 35 1 0 3 36 1 0 3 37 1 0 3 38 1 0 4 39 1 6 5 40 1 0 5 41 1 0 6 42 1 0 6 43 1 0 10 44 1 0 11 45 1 0 11 46 1 0 12 47 1 0 12 48 1 0 14 49 1 0 14 50 1 0 14 51 1 0 15 52 1 1 16 53 1 0 16 54 1 0 17 55 1 0 17 56 1 0 18 57 1 6 20 58 1 0 20 59 1 0 20 60 1 0 21 61 1 0 21 62 1 0 22 63 1 0 22 64 1 0 26 65 1 0 26 66 1 0 26 67 1 0 27 68 1 0 27 69 1 0 27 70 1 0 28 71 1 6 29 72 1 0 29 73 1 0 30 74 1 0 30 75 1 0 32 76 1 0 32 77 1 0 32 78 1 0 33 79 1 6 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 NPC607951 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	27154
0.1-0.2	19787
0.2-0.3	2347
0.3-0.4	404
0.4-0.5	90
0.5-0.6	41
0.6-0.7	24
0.7-0.8	0
0.8-0.85	3
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	NPC192744
0.8448	Intermediate Similarity	NPC601275
0.8167	Intermediate Similarity	NPC608379
0.8103	Intermediate Similarity	NPC201655
0.7258	Intermediate Similarity	NPC474719
0.7143	Intermediate Similarity	NPC611139
0.7069	Intermediate Similarity	NPC68828
0.6923	Remote Similarity	NPC600907
0.6613	Remote Similarity	NPC264317
0.6613	Remote Similarity	NPC294438
0.6562	Remote Similarity	NPC4309
0.6508	Remote Similarity	NPC488164
0.6508	Remote Similarity	NPC264005
0.65	Remote Similarity	NPC246445
0.6479	Remote Similarity	NPC605397
0.6406	Remote Similarity	NPC271974
0.6406	Remote Similarity	NPC247312
0.6364	Remote Similarity	NPC160506
0.6324	Remote Similarity	NPC603461
0.6269	Remote Similarity	NPC600004
0.6269	Remote Similarity	NPC602147
0.625	Remote Similarity	NPC488506
0.625	Remote Similarity	NPC220498
0.619	Remote Similarity	NPC119743
0.6176	Remote Similarity	NPC606727
0.6119	Remote Similarity	NPC603784
0.6029	Remote Similarity	NPC478841
0.6029	Remote Similarity	NPC488166
0.6027	Remote Similarity	NPC611262
0.6	Remote Similarity	NPC24772
0.6	Remote Similarity	NPC213832
0.589	Remote Similarity	NPC606354
0.5882	Remote Similarity	NPC488165
0.5846	Remote Similarity	NPC80590
0.5833	Remote Similarity	NPC43300
0.5821	Remote Similarity	NPC151191
0.5821	Remote Similarity	NPC16377
0.5781	Remote Similarity	NPC472740
0.5781	Remote Similarity	NPC69101
0.5758	Remote Similarity	NPC211162
0.5758	Remote Similarity	NPC183374
0.5753	Remote Similarity	NPC602512
0.5672	Remote Similarity	NPC195395
0.5652	Remote Similarity	NPC486704
0.5647	Remote Similarity	NPC487492
0.5588	Remote Similarity	NPC606726
0.5522	Remote Similarity	NPC291373
0.5507	Remote Similarity	NPC475061
0.5507	Remote Similarity	NPC488213
0.5469	Remote Similarity	NPC201459
0.5441	Remote Similarity	NPC277399
0.5397	Remote Similarity	NPC604288
0.5385	Remote Similarity	NPC63020
0.5385	Remote Similarity	NPC108131
0.5373	Remote Similarity	NPC30583
0.5352	Remote Similarity	NPC606728
0.5352	Remote Similarity	NPC607677
0.5352	Remote Similarity	NPC608881
0.5312	Remote Similarity	NPC159497
0.5256	Remote Similarity	NPC486709
0.5217	Remote Similarity	NPC274050
0.5217	Remote Similarity	NPC193907
0.5217	Remote Similarity	NPC162632
0.5211	Remote Similarity	NPC244356
0.5211	Remote Similarity	NPC224060
0.5152	Remote Similarity	NPC103754
0.5143	Remote Similarity	NPC2783
0.5139	Remote Similarity	NPC169933
0.5139	Remote Similarity	NPC601176
0.5075	Remote Similarity	NPC474484
0.507	Remote Similarity	NPC269360
0.5062	Remote Similarity	NPC486699

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC607951 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6029
0.1-0.2	3037
0.2-0.3	78
0.3-0.4	3
0.4-0.5	1
0.5-0.6	0
0.6-0.7	2
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
0.6613	Remote Similarity	NPD7520	Phase 1
0.6364	Remote Similarity	NPD8035	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