NPASS Compound

Natural Product: NPC601964

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 76 80 0 0 0 0 0 0 0 0999 V2000 6.7499 -0.7297 1.8620 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4599 -0.5075 1.2299 N 0 0 0 0 0 0 0 0 0 0 0 0 5.2711 -0.7926 -0.1390 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3951 -1.2938 -0.8197 C 0 0 0 0 0 0 0 0 0 0 0 0 6.3235 -1.6061 -2.1570 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1291 -1.4168 -2.8104 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0408 -0.9248 -2.1238 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0867 -0.6035 -0.7811 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8988 -0.0935 -0.1406 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7822 0.2391 1.0547 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7015 0.0736 -0.8861 O 0 0 0 0 0 0 0 0 0 0 0 0 0.5060 0.5530 -0.3538 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5154 -0.5935 -0.1804 C 0 0 1 0 0 0 0 0 0 0 0 0 0.3438 -1.7608 0.2618 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4947 -0.0961 0.7928 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7867 0.5448 1.8316 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.2663 1.0183 0.1024 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.2771 1.4628 1.0979 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3891 0.8170 1.4331 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2380 1.4858 2.4676 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4782 1.7395 1.9310 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.8665 -0.4837 0.8860 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6690 -1.3852 0.6611 C 0 0 2 0 0 0 0 0 0 0 0 0 -3.4418 -1.6487 -0.6827 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.0608 -2.6952 1.2488 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.2127 -3.2056 1.1694 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8706 -3.2170 1.8986 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7272 -4.6428 2.3693 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.9672 -2.2541 2.0005 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4599 -1.0093 1.4344 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.4399 2.0744 -0.4892 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.9928 2.0263 -1.9204 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3746 0.9688 -2.8859 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0225 3.4252 -2.5717 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0339 1.8318 -0.8138 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9011 2.8921 -0.7290 O 0 0 0 0 0 0 0 0 0 0 0 0 2.0177 2.8881 -1.5298 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0453 3.9958 -1.4345 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3052 2.0153 -2.3888 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7571 -0.3553 2.8852 H 0 0 0 0 0 0 0 0 0 0 0 0 7.5605 -0.2244 1.2915 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9678 -1.8184 1.8699 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7232 -0.1378 1.8472 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3409 -1.4488 -0.3221 H 0 0 0 0 0 0 0 0 0 0 0 0 7.1871 -1.9959 -2.6995 H 0 0 0 0 0 0 0 0 0 0 0 0 5.0398 -1.6539 -3.8668 H 0 0 0 0 0 0 0 0 0 0 0 0 3.0969 -0.7737 -2.6341 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7584 0.7524 0.7486 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9337 -0.9140 -1.1523 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.1842 -2.7308 0.1472 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1751 -1.8169 -0.5064 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8394 -1.6319 1.2180 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4035 -0.1066 2.4680 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8816 0.5985 -0.7499 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1020 2.3938 1.6005 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3032 0.7949 3.3590 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7245 2.3835 2.8297 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.7795 0.9046 1.4654 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6005 -0.8819 1.5877 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.3786 -0.3005 -0.0924 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2503 -1.3567 -1.1924 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6847 -4.9849 2.2129 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3766 -5.3174 1.7822 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0462 -4.7002 3.4220 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0057 -2.4195 2.4575 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8726 -0.4379 2.3314 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6301 3.0839 -0.0093 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2528 0.3681 -2.6599 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4416 0.3628 -3.0967 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6002 1.3653 -3.9270 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.6845 3.3710 -3.6178 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4924 4.1458 -1.9474 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0919 3.7644 -2.6096 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7600 4.7283 -0.6690 H 0 0 0 0 0 0 0 0 0 0 0 0 3.1409 4.4211 -2.4526 H 0 0 0 0 0 0 0 0 0 0 0 0 4.0011 3.4774 -1.2137 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 1 0 12 13 1 0 13 14 1 0 13 15 1 0 15 16 1 1 15 17 1 0 17 18 1 0 18 19 2 0 19 20 1 0 20 21 1 0 19 22 1 0 22 23 1 0 23 24 1 6 23 25 1 0 25 26 2 0 25 27 1 0 27 28 1 0 27 29 2 0 29 30 1 0 17 31 1 0 31 32 1 0 32 33 1 0 32 34 1 0 32 35 1 0 35 36 1 1 36 37 1 0 37 38 1 0 37 39 2 0 8 3 1 0 35 12 1 0 30 15 1 0 35 31 1 0 30 23 1 0 1 40 1 0 1 41 1 0 1 42 1 0 2 43 1 0 4 44 1 0 5 45 1 0 6 46 1 0 7 47 1 0 12 48 1 1 13 49 1 6 14 50 1 0 14 51 1 0 14 52 1 0 16 53 1 0 17 54 1 6 18 55 1 0 20 56 1 0 20 57 1 0 21 58 1 0 22 59 1 0 22 60 1 0 24 61 1 0 28 62 1 0 28 63 1 0 28 64 1 0 29 65 1 0 30 66 1 1 31 67 1 1 33 68 1 0 33 69 1 0 33 70 1 0 34 71 1 0 34 72 1 0 34 73 1 0 38 74 1 0 38 75 1 0 38 76 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 NPC601964 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	9059
0.1-0.2	39144
0.2-0.3	1482
0.3-0.4	86
0.4-0.5	36
0.5-0.6	28
0.6-0.7	16
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
0.75	Intermediate Similarity	NPC112752
0.75	Intermediate Similarity	NPC311054
0.7024	Intermediate Similarity	NPC472398
0.7024	Intermediate Similarity	NPC600915
0.6897	Remote Similarity	NPC176371
0.6897	Remote Similarity	NPC136573
0.6897	Remote Similarity	NPC609007
0.686	Remote Similarity	NPC21483
0.686	Remote Similarity	NPC198205
0.686	Remote Similarity	NPC138641
0.686	Remote Similarity	NPC611243
0.6667	Remote Similarity	NPC90358
0.6667	Remote Similarity	NPC22571
0.6667	Remote Similarity	NPC107828
0.6629	Remote Similarity	NPC601392
0.6556	Remote Similarity	NPC198390
0.6556	Remote Similarity	NPC601559
0.6484	Remote Similarity	NPC283875
0.6098	Remote Similarity	NPC472758
0.6049	Remote Similarity	NPC472397
0.5882	Remote Similarity	NPC5991
0.5882	Remote Similarity	NPC196500
0.5882	Remote Similarity	NPC471108
0.5882	Remote Similarity	NPC5989
0.5854	Remote Similarity	NPC171905
0.5833	Remote Similarity	NPC471125
0.5765	Remote Similarity	NPC275696
0.5765	Remote Similarity	NPC255081
0.5747	Remote Similarity	NPC243902
0.5714	Remote Similarity	NPC157252
0.5682	Remote Similarity	NPC478999
0.5632	Remote Similarity	NPC471128
0.5632	Remote Similarity	NPC471126
0.5618	Remote Similarity	NPC484333
0.5581	Remote Similarity	NPC145182
0.5579	Remote Similarity	NPC602154
0.5556	Remote Similarity	NPC145238
0.5506	Remote Similarity	NPC22628
0.5368	Remote Similarity	NPC11410
0.5368	Remote Similarity	NPC600144
0.5333	Remote Similarity	NPC600005
0.5306	Remote Similarity	NPC603807
0.5158	Remote Similarity	NPC469647
0.5158	Remote Similarity	NPC469648
0.5155	Remote Similarity	NPC479001
0.5155	Remote Similarity	NPC479002
0.5152	Remote Similarity	NPC600480
0.5052	Remote Similarity	NPC482198

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC601964 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3192
0.1-0.2	5885
0.2-0.3	73
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