NPASS Compound

Natural Product: NPC611408

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 89 94 0 0 0 0 0 0 0 0999 V2000 8.7188 -0.1807 2.7298 C 0 0 0 0 0 0 0 0 0 0 0 0 8.2749 0.6225 1.6768 O 0 0 0 0 0 0 0 0 0 0 0 0 7.5127 -0.0733 0.7697 C 0 0 1 0 0 0 0 0 0 0 0 0 6.0979 0.4700 0.7631 C 0 0 0 0 0 0 0 0 0 0 0 0 5.2768 -0.2038 -0.3118 C 0 0 2 0 0 0 0 0 0 0 0 0 4.1040 -0.6630 0.2373 O 0 0 0 0 0 0 0 0 0 0 0 0 2.9611 -0.0764 -0.2996 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0898 -1.0480 -0.9897 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7903 -1.3844 -0.3946 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2366 -0.4840 0.6527 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6097 -1.0745 2.0067 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8213 0.8987 0.5712 C 0 0 2 0 0 0 0 0 0 0 0 0 0.5018 1.6202 -0.6923 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8710 1.3081 -1.2423 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7311 0.8691 -0.0970 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.2782 -0.3963 0.5543 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9494 -0.4474 1.9156 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1128 0.4765 2.0302 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0049 0.5260 0.8152 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.9197 1.7122 1.0034 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6562 -0.7561 0.5022 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.8940 -1.1149 1.1686 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6336 -0.5574 2.0900 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7924 -1.3814 2.3819 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6992 -1.1017 3.2377 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.7289 -2.5010 1.5751 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.5841 -2.4075 0.8005 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.9284 -0.6712 -0.9954 C 0 0 1 0 0 0 0 0 0 0 0 0 -5.8239 0.3447 -1.3216 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.9417 0.1428 -2.1227 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.8563 1.2892 -2.4262 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1460 -0.9967 -2.5644 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.5389 -0.2257 -1.4620 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1887 0.8062 -0.4525 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.5078 2.0408 -1.0212 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3106 0.7572 0.7586 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0090 -1.1817 -0.9698 O 0 0 0 0 0 0 0 0 0 0 0 0 7.0696 -0.5630 -1.6085 C 0 0 1 0 0 0 0 0 0 0 0 0 6.6486 0.6510 -2.4039 C 0 0 0 0 0 0 0 0 0 0 0 0 8.1272 -0.1108 -0.6061 C 0 0 2 0 0 0 0 0 0 0 0 0 9.1473 -1.0853 -0.5716 O 0 0 0 0 0 0 0 0 0 0 0 0 9.3203 0.4736 3.4000 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8552 -0.5352 3.3400 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3654 -1.0058 2.4019 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4384 -1.1398 1.1135 H 0 0 0 0 0 0 0 0 0 0 0 0 5.6913 0.3004 1.7792 H 0 0 0 0 0 0 0 0 0 0 0 0 6.1452 1.5697 0.6110 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0153 0.5569 -1.0803 H 0 0 0 0 0 0 0 0 0 0 0 0 3.3445 0.6517 -1.0762 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9274 -0.7685 -2.0759 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6840 -2.0098 -1.0862 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0100 -1.4687 -1.1939 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7820 -2.4313 0.0368 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8370 -0.3182 2.7601 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1468 -1.8157 2.3410 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5589 -1.6747 1.8844 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4347 1.4828 1.4314 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2886 1.4655 -1.4773 H 0 0 0 0 0 0 0 0 0 0 0 0 0.5634 2.7244 -0.4636 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.3021 2.2513 -1.6385 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8523 0.5968 -2.0826 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6417 1.6784 0.6830 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.5912 -1.3187 0.0226 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.1613 -1.4909 2.2260 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.1798 -0.0659 2.6476 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7462 0.0919 2.8761 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8354 1.5084 2.3246 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9339 1.5794 0.6219 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.8974 2.0906 2.0726 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5338 2.6284 0.4528 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8943 -1.5768 0.6280 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.4415 0.3754 2.5898 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7482 -2.4764 -0.2815 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.9005 -3.2515 1.0714 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1910 -1.6554 -1.4309 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.3964 2.2467 -2.1353 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.0042 1.3473 -3.5341 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8184 1.1456 -1.9208 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7045 0.1991 -2.4880 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9163 -1.1067 -1.5073 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4165 1.9872 -2.0218 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7236 1.7915 0.8021 H 0 0 0 0 0 0 0 0 0 0 0 0 2.4950 0.3168 1.7603 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5371 -1.2864 -2.3215 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4584 0.8179 -3.1665 H 0 0 0 0 0 0 0 0 0 0 0 0 6.6417 1.5604 -1.7834 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7271 0.4884 -2.9900 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5420 0.8678 -0.8977 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3668 -1.2469 -1.5322 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 7 8 1 0 8 9 1 0 9 10 1 0 10 11 1 1 10 12 1 0 12 13 1 0 13 14 1 0 14 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 2 0 23 24 1 0 24 25 2 0 24 26 1 0 26 27 1 0 21 28 1 0 28 29 1 0 29 30 1 0 30 31 1 0 30 32 2 0 28 33 1 0 33 34 1 0 34 35 1 6 12 36 1 0 5 37 1 0 37 38 1 0 38 39 1 0 38 40 1 0 40 41 1 0 40 3 1 0 36 7 1 0 16 10 1 0 34 19 1 0 34 15 1 0 27 22 1 0 1 42 1 0 1 43 1 0 1 44 1 0 3 45 1 1 4 46 1 0 4 47 1 0 5 48 1 6 7 49 1 6 8 50 1 0 8 51 1 0 9 52 1 0 9 53 1 0 11 54 1 0 11 55 1 0 11 56 1 0 12 57 1 1 13 58 1 0 13 59 1 0 14 60 1 0 14 61 1 0 15 62 1 1 16 63 1 6 17 64 1 0 17 65 1 0 18 66 1 0 18 67 1 0 20 68 1 0 20 69 1 0 20 70 1 0 21 71 1 6 23 72 1 0 27 73 1 0 27 74 1 0 28 75 1 6 31 76 1 0 31 77 1 0 31 78 1 0 33 79 1 0 33 80 1 0 35 81 1 0 36 82 1 0 36 83 1 0 38 84 1 6 39 85 1 0 39 86 1 0 39 87 1 0 40 88 1 6 41 89 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 NPC611408 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	15285
0.1-0.2	30034
0.2-0.3	4184
0.3-0.4	179
0.4-0.5	111
0.5-0.6	34
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	4

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC103534
1.0	High Similarity	NPC44899
1.0	High Similarity	NPC304260
1.0	High Similarity	NPC29639
0.7857	Intermediate Similarity	NPC488935
0.7857	Intermediate Similarity	NPC5883
0.7857	Intermediate Similarity	NPC488936
0.7778	Intermediate Similarity	NPC99080
0.7683	Intermediate Similarity	NPC84949
0.7683	Intermediate Similarity	NPC480562
0.7683	Intermediate Similarity	NPC74945
0.7683	Intermediate Similarity	NPC31354
0.7683	Intermediate Similarity	NPC69576
0.6842	Remote Similarity	NPC488943
0.6842	Remote Similarity	NPC488938
0.6842	Remote Similarity	NPC488937
0.6842	Remote Similarity	NPC488942
0.6737	Remote Similarity	NPC475219
0.6517	Remote Similarity	NPC483822
0.6436	Remote Similarity	NPC488945
0.6436	Remote Similarity	NPC488946
0.6373	Remote Similarity	NPC488947
0.6341	Remote Similarity	NPC119855
0.6154	Remote Similarity	NPC484202
0.6154	Remote Similarity	NPC93883
0.6136	Remote Similarity	NPC471633
0.6	Remote Similarity	NPC479356
0.6	Remote Similarity	NPC34390
0.6	Remote Similarity	NPC479355
0.6	Remote Similarity	NPC477580
0.5934	Remote Similarity	NPC199428
0.5934	Remote Similarity	NPC109448
0.5934	Remote Similarity	NPC152615
0.5934	Remote Similarity	NPC310341
0.587	Remote Similarity	NPC180079
0.5745	Remote Similarity	NPC193893
0.5684	Remote Similarity	NPC72260
0.5657	Remote Similarity	NPC55532
0.5604	Remote Similarity	NPC99620
0.5532	Remote Similarity	NPC290693
0.5392	Remote Similarity	NPC486146
0.5368	Remote Similarity	NPC484212
0.5319	Remote Similarity	NPC5311
0.53	Remote Similarity	NPC603096
0.5258	Remote Similarity	NPC268326
0.5258	Remote Similarity	NPC153085
0.5248	Remote Similarity	NPC231518
0.5248	Remote Similarity	NPC488944
0.5234	Remote Similarity	NPC74259
0.5234	Remote Similarity	NPC475419
0.5196	Remote Similarity	NPC486143
0.5196	Remote Similarity	NPC486142
0.5196	Remote Similarity	NPC486149
0.5185	Remote Similarity	NPC474908
0.5152	Remote Similarity	NPC157817
0.5152	Remote Similarity	NPC173555
0.5093	Remote Similarity	NPC120390
0.5053	Remote Similarity	NPC481208
0.5052	Remote Similarity	NPC250556
0.505	Remote Similarity	NPC115349
0.5047	Remote Similarity	NPC329636
0.5046	Remote Similarity	NPC486134
0.5046	Remote Similarity	NPC486141
0.5045	Remote Similarity	NPC474423

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC611408 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6187
0.1-0.2	2838
0.2-0.3	109
0.3-0.4	5
0.4-0.5	1
0.5-0.6	7
0.6-0.7	3
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
0.6667	Remote Similarity	NPD8377	Phase 4
0.6082	Remote Similarity	NPD8378	Pre-clinical
0.6082	Remote Similarity	NPD8379	Approved
0.5684	Remote Similarity	NPD8294	Phase 4
0.5248	Remote Similarity	NPD8033	Approved
0.5208	Remote Similarity	NPD8335	Phase 4
0.5155	Remote Similarity	NPD7516	Pre-clinical
0.5155	Remote Similarity	NPD8380	Approved
0.5152	Remote Similarity	NPD8296	Phase 4
0.5052	Remote Similarity	NPD7507	Pre-clinical

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