NPASS Compound

Natural Product: NPC607901

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 48 50 0 0 0 0 0 0 0 0999 V2000 -6.2576 1.2033 -2.7060 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5692 0.7576 -1.8419 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.7940 0.2558 -0.8690 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4269 0.4264 -0.8417 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6006 -0.0737 0.1386 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1331 0.2082 0.0298 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3817 -0.8653 -0.6706 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.5299 -2.1967 0.0870 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0840 -0.5383 -0.6895 C 0 0 2 0 0 0 0 0 0 0 0 0 1.9188 -1.5889 -1.3797 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5609 -0.2048 0.6791 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0391 0.1069 0.6610 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9732 -0.8588 0.8726 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3183 -0.4898 0.8410 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6836 0.8085 0.6020 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7382 1.8114 0.3811 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4167 1.4097 0.4203 C 0 0 0 0 0 0 0 0 0 0 0 0 5.3728 3.0173 0.1680 O 0 0 0 0 0 0 0 0 0 0 0 0 6.7088 2.8717 0.6617 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9132 1.4826 0.5091 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.1720 -0.7841 1.1449 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5527 -0.9950 1.1786 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.3450 -0.4921 0.2036 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7400 -0.6409 0.1344 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2105 2.3501 -2.9214 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.4183 1.0666 -2.5718 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1736 0.8163 -3.7954 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.9880 1.0053 -1.6716 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0429 1.1877 -0.4758 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7968 0.2882 1.0950 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.7779 -1.0905 -1.6882 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3045 -2.8966 -0.1756 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4441 -2.0032 1.1787 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.4770 -2.6964 -0.1071 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1901 0.3833 -1.3413 H 0 0 0 0 0 0 0 0 0 0 0 0 2.8520 -1.0833 -1.7555 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3426 -1.9704 -2.2607 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2020 -2.4199 -0.7451 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3480 -1.0339 1.3904 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1051 0.7031 1.0808 H 0 0 0 0 0 0 0 0 0 0 0 0 3.6765 -1.8796 1.0576 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0805 -1.2337 1.0071 H 0 0 0 0 0 0 0 0 0 0 0 0 2.6639 2.1997 0.2446 H 0 0 0 0 0 0 0 0 0 0 0 0 6.7091 3.0521 1.7631 H 0 0 0 0 0 0 0 0 0 0 0 0 7.4391 3.4900 0.1049 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5496 -1.1935 1.9350 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.9995 -1.5608 1.9769 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2602 -0.1119 0.8343 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 1 0 6 7 1 0 7 8 1 0 7 9 1 0 9 10 1 0 9 11 1 0 11 12 1 0 12 13 2 0 13 14 1 0 14 15 2 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 1 0 19 20 1 0 5 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 23 3 1 0 17 12 1 0 20 15 1 0 1 25 1 0 1 26 1 0 1 27 1 0 4 28 1 0 6 29 1 0 6 30 1 0 7 31 1 6 8 32 1 0 8 33 1 0 8 34 1 0 9 35 1 6 10 36 1 0 10 37 1 0 10 38 1 0 11 39 1 0 11 40 1 0 13 41 1 0 14 42 1 0 17 43 1 0 19 44 1 0 19 45 1 0 21 46 1 0 22 47 1 0 24 48 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 NPC607901 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	21219
0.1-0.2	22560
0.2-0.3	4962
0.3-0.4	820
0.4-0.5	218
0.5-0.6	41
0.6-0.7	12
0.7-0.8	0
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
0.95-1	2

Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC274356
1.0	High Similarity	NPC101748
0.84	Intermediate Similarity	NPC487677
0.84	Intermediate Similarity	NPC487675
0.8	Intermediate Similarity	NPC227217
0.8	Intermediate Similarity	NPC117780
0.7778	Intermediate Similarity	NPC487679
0.7778	Intermediate Similarity	NPC487678
0.7692	Intermediate Similarity	NPC46880
0.7547	Intermediate Similarity	NPC487681
0.7451	Intermediate Similarity	NPC284464
0.7447	Intermediate Similarity	NPC249788
0.7407	Intermediate Similarity	NPC106739
0.7407	Intermediate Similarity	NPC161249
0.7273	Intermediate Similarity	NPC471505
0.7209	Intermediate Similarity	NPC165133
0.7209	Intermediate Similarity	NPC242885
0.7209	Intermediate Similarity	NPC95614
0.7209	Intermediate Similarity	NPC232316
0.7111	Intermediate Similarity	NPC344161
0.6977	Remote Similarity	NPC80241
0.6977	Remote Similarity	NPC301641
0.6977	Remote Similarity	NPC485483
0.6724	Remote Similarity	NPC282291
0.6724	Remote Similarity	NPC166137
0.6724	Remote Similarity	NPC169973
0.6471	Remote Similarity	NPC485480
0.6327	Remote Similarity	NPC56214
0.6275	Remote Similarity	NPC607444
0.6078	Remote Similarity	NPC127587
0.6	Remote Similarity	NPC28398
0.6	Remote Similarity	NPC487676
0.5926	Remote Similarity	NPC487680
0.5769	Remote Similarity	NPC485482
0.5614	Remote Similarity	NPC142547
0.5614	Remote Similarity	NPC228469
0.5556	Remote Similarity	NPC104077
0.5556	Remote Similarity	NPC165106
0.5556	Remote Similarity	NPC219671
0.5556	Remote Similarity	NPC156840
0.5556	Remote Similarity	NPC216223
0.5556	Remote Similarity	NPC147616
0.551	Remote Similarity	NPC40352
0.551	Remote Similarity	NPC85488
0.551	Remote Similarity	NPC213711
0.55	Remote Similarity	NPC291101
0.55	Remote Similarity	NPC266197
0.5472	Remote Similarity	NPC196937
0.5424	Remote Similarity	NPC227002
0.5333	Remote Similarity	NPC300776
0.5333	Remote Similarity	NPC176814
0.5333	Remote Similarity	NPC4982
0.5333	Remote Similarity	NPC606629
0.5323	Remote Similarity	NPC145569
0.5273	Remote Similarity	NPC30951
0.5273	Remote Similarity	NPC474288
0.5208	Remote Similarity	NPC8547
0.52	Remote Similarity	NPC57490
0.5192	Remote Similarity	NPC31344
0.5192	Remote Similarity	NPC317769
0.5167	Remote Similarity	NPC88640
0.5167	Remote Similarity	NPC101153
0.5167	Remote Similarity	NPC193666
0.5167	Remote Similarity	NPC123526
0.5167	Remote Similarity	NPC608725
0.5102	Remote Similarity	NPC477886
0.5098	Remote Similarity	NPC299406
0.5094	Remote Similarity	NPC476748
0.5091	Remote Similarity	NPC232275
0.5088	Remote Similarity	NPC143895
0.5079	Remote Similarity	NPC31751
0.5079	Remote Similarity	NPC43514
0.5075	Remote Similarity	NPC604694

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC607901 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	3695
0.1-0.2	5068
0.2-0.3	358
0.3-0.4	23
0.4-0.5	4
0.5-0.6	1
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
0.5556	Remote Similarity	NPD5283	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