NPASS Compound

Natural Product: NPC608433

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 73 76 0 0 0 0 0 0 0 0999 V2000 7.7004 1.1738 0.1755 C 0 0 0 0 0 0 0 0 0 0 0 0 6.7980 1.2977 -1.0139 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5604 0.5038 -0.7942 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4507 -0.1188 0.2921 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5430 0.4176 -1.7085 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3811 -0.3700 -1.4076 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6790 0.1698 -0.2247 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1917 1.1590 0.2810 O 0 0 0 0 0 0 0 0 0 0 0 0 1.4587 -0.3311 0.3953 C 0 0 1 0 0 0 0 0 0 0 0 0 1.0225 -1.5936 -0.0897 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6766 -2.7802 0.0266 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7738 -2.7919 0.6363 O 0 0 0 0 0 0 0 0 0 0 0 0 1.1964 -4.0730 -0.5123 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1179 -3.9633 -1.2198 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4003 -0.2552 1.8918 C 0 0 1 0 0 0 0 0 0 0 0 0 2.5701 0.2567 2.6106 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0970 0.4286 2.2849 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6849 0.1602 1.0722 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.0101 0.8179 0.8835 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.8903 0.7324 2.0655 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2155 1.3942 1.7433 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.7669 0.5051 0.6291 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8476 -0.1685 0.8056 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4401 -1.0583 -0.2179 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4827 -1.6938 -0.0229 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.7022 -1.1267 -1.4682 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6046 -0.4100 -1.5896 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.9997 0.4787 -0.6263 C 0 0 1 0 0 0 0 0 0 0 0 0 -4.1153 1.8759 -1.3174 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5535 0.2046 -0.3900 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.3068 -1.1500 -0.3397 F 0 0 0 0 0 0 0 0 0 0 0 0 -1.6700 0.7587 -1.5060 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.5706 2.1254 -1.4960 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2890 0.1833 -1.3254 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2711 0.5853 -0.0016 C 0 0 2 0 0 0 0 0 0 0 0 0 0.7445 1.9844 0.0995 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6541 2.0879 0.8235 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7334 0.9276 -0.1345 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3382 0.3470 0.8467 H 0 0 0 0 0 0 0 0 0 0 0 0 7.2902 1.0446 -1.9724 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5039 2.3656 -1.0954 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7364 -0.2400 -2.3376 H 0 0 0 0 0 0 0 0 0 0 0 0 3.7545 -1.3850 -1.3435 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1259 -4.7776 0.3414 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9603 -4.4733 -1.2036 H 0 0 0 0 0 0 0 0 0 0 0 0 0.0634 -3.4772 -2.2193 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8898 -3.4610 -0.6370 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4539 -4.9995 -1.4556 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2497 -1.3269 2.2392 H 0 0 0 0 0 0 0 0 0 0 0 0 2.7187 1.3219 2.7180 H 0 0 0 0 0 0 0 0 0 0 0 0 2.5056 -0.1383 3.6719 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5303 -0.1781 2.2419 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2253 1.4809 2.5742 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3463 -0.0797 3.1944 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8100 -0.9486 0.9822 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8349 1.8931 0.6561 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.4034 1.2027 2.9426 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.1188 -0.3432 2.2517 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9009 1.4745 2.5738 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.0089 2.3940 1.3121 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.3895 -0.1028 1.7629 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0569 -1.7654 -2.2936 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.1094 -0.5336 -2.5783 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6983 1.7177 -2.3283 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.6869 2.6663 -0.7222 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1943 2.1063 -1.4627 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0150 0.3698 -2.4984 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4502 2.5548 -2.3509 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.2752 -0.9193 -1.4049 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3513 0.6253 -2.1324 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4174 2.2939 -0.7276 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3043 2.2011 1.0335 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0679 2.7455 0.1112 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 3 5 1 0 5 6 1 0 6 7 1 0 7 8 2 0 7 9 1 0 9 10 1 1 10 11 1 0 11 12 2 0 11 13 1 0 13 14 1 0 9 15 1 0 15 16 1 0 15 17 1 0 17 18 1 0 18 19 1 0 19 20 1 0 20 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 2 0 27 28 1 0 28 29 1 6 28 30 1 0 30 31 1 1 30 32 1 0 32 33 1 0 32 34 1 0 34 35 1 0 35 36 1 6 35 9 1 0 35 18 1 0 30 19 1 0 28 22 1 0 1 37 1 0 1 38 1 0 1 39 1 0 2 40 1 0 2 41 1 0 6 42 1 0 6 43 1 0 13 44 1 0 13 45 1 0 14 46 1 0 14 47 1 0 14 48 1 0 15 49 1 1 16 50 1 0 16 51 1 0 16 52 1 0 17 53 1 0 17 54 1 0 18 55 1 6 19 56 1 6 20 57 1 0 20 58 1 0 21 59 1 0 21 60 1 0 23 61 1 0 26 62 1 0 27 63 1 0 29 64 1 0 29 65 1 0 29 66 1 0 32 67 1 6 33 68 1 0 34 69 1 0 34 70 1 0 36 71 1 0 36 72 1 0 36 73 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 NPC608433 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	16233
0.1-0.2	32143
0.2-0.3	1472
0.3-0.4	8
0.4-0.5	1
0.5-0.6	1
0.6-0.7	0
0.7-0.8	2
0.8-0.85	0
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	NPC481929
0.5467	Remote Similarity	NPC331613

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC608433 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	6244
0.1-0.2	2710
0.2-0.3	110
0.3-0.4	40
0.4-0.5	9
0.5-0.6	27
0.6-0.7	4
0.7-0.8	2
0.8-0.85	1
0.85-0.9	0
0.9-0.95	1
0.95-1	2

Similarity Score	Similarity Level	Drug ID	Developmental Stage
1.0	High Similarity	NPD7101	Phase 4
1.0	High Similarity	NPD7102	Phase 4
0.9231	High Similarity	NPD7290	Pre-clinical
0.8308	Intermediate Similarity	NPD6335	Phase 4
0.75	Intermediate Similarity	NPD6014	Approved
0.7222	Intermediate Similarity	NPD6883	Phase 4
0.6622	Remote Similarity	NPD6617	Phase 4
0.6173	Remote Similarity	NPD7236	Phase 4
0.6133	Remote Similarity	NPD6313	Phase 4
0.6133	Remote Similarity	NPD6314	Approved
0.5952	Remote Similarity	NPD6784	Approved
0.5952	Remote Similarity	NPD6785	Phase 4
0.5921	Remote Similarity	NPD6013	Phase 4
0.5854	Remote Similarity	NPD7492	Phase 4
0.5789	Remote Similarity	NPD7100	Phase 4
0.5769	Remote Similarity	NPD5247	Approved
0.5769	Remote Similarity	NPD5249	Phase 3
0.5714	Remote Similarity	NPD7078	Phase 4
0.5696	Remote Similarity	NPD6319	Phase 4
0.5616	Remote Similarity	NPD5222	Phase 4
0.5541	Remote Similarity	NPD5167	Pre-clinical
0.5541	Remote Similarity	NPD5169	Approved
0.5526	Remote Similarity	NPD5290	Phase 2
0.55	Remote Similarity	NPD5250	Phase 4
0.55	Remote Similarity	NPD5251	Phase 4
0.5488	Remote Similarity	NPD8130	Phase 1
0.5467	Remote Similarity	NPD5216	Phase 2
0.5467	Remote Similarity	NPD5217	Approved
0.5467	Remote Similarity	NPD5225	Phase 4
0.5467	Remote Similarity	NPD5226	Phase 4
0.5432	Remote Similarity	NPD5248	Approved
0.5309	Remote Similarity	NPD6015	Phase 4
0.5263	Remote Similarity	NPD4634	Phase 4
0.5256	Remote Similarity	NPD6614	Phase 4
0.525	Remote Similarity	NPD6336	Discontinued
0.5195	Remote Similarity	NPD5141	Phase 2
0.5122	Remote Similarity	NPD6317	Phase 4

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