NPASS Compound

Natural Product: NPC610511

Natural Product ID	NPC610511
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	GJFHZVPRFLHEBR-KETROQBRSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL4173326
PubChem CID	n.a.
Chemical Classification	CHEMONTID:0000000 [Organic compounds]

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 59 61 0 0 0 0 0 0 0 0999 V2000 7.7698 -0.0293 -0.9645 C 0 0 0 0 0 0 0 0 0 0 0 0 7.3527 1.2518 -0.3601 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3813 2.1829 0.1563 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0854 1.5671 -0.2794 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0537 0.6393 -0.7953 C 0 0 0 0 0 0 0 0 0 0 0 0 4.0869 0.2083 0.2924 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1031 -0.7252 -0.3721 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6084 -1.9421 -1.0107 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8348 -0.3651 -0.3426 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7778 -1.2017 -0.9598 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3080 -1.5685 -0.0201 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5246 -0.9200 -0.1045 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5827 -1.1941 0.7249 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8928 -0.5455 0.6908 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.8121 -1.3374 -0.2346 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1723 -0.7450 -0.0473 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.1901 -1.4107 0.2256 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.2438 0.7170 -0.2089 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4423 1.3194 -0.4898 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5683 0.5270 -0.6154 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.4929 2.6918 -0.6388 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3344 3.4148 -0.5001 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.4208 4.7961 -0.6565 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1304 2.7888 -0.2158 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0584 1.4068 -0.0620 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.8578 0.7742 0.2221 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.3628 -2.1789 1.6747 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3888 -2.5278 2.5684 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1699 -2.8356 1.7796 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.1244 -2.5340 0.9270 C 0 0 0 0 0 0 0 0 0 0 0 0 1.0885 -3.2337 1.0687 O 0 0 0 0 0 0 0 0 0 0 0 0 8.8760 -0.1213 -1.0407 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3617 -0.0648 -2.0067 H 0 0 0 0 0 0 0 0 0 0 0 0 7.3249 -0.8991 -0.4288 H 0 0 0 0 0 0 0 0 0 0 0 0 9.1957 2.3747 -0.5432 H 0 0 0 0 0 0 0 0 0 0 0 0 8.8156 1.8491 1.1195 H 0 0 0 0 0 0 0 0 0 0 0 0 7.9181 3.1831 0.3809 H 0 0 0 0 0 0 0 0 0 0 0 0 5.7842 2.5146 0.1685 H 0 0 0 0 0 0 0 0 0 0 0 0 4.4254 1.1216 -1.5814 H 0 0 0 0 0 0 0 0 0 0 0 0 5.5367 -0.2842 -1.1593 H 0 0 0 0 0 0 0 0 0 0 0 0 4.6152 -0.3500 1.1009 H 0 0 0 0 0 0 0 0 0 0 0 0 3.5763 1.0616 0.7777 H 0 0 0 0 0 0 0 0 0 0 0 0 3.8633 -1.8066 -2.0842 H 0 0 0 0 0 0 0 0 0 0 0 0 4.5982 -2.2039 -0.5311 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9748 -2.8196 -0.8296 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5462 0.5771 0.1493 H 0 0 0 0 0 0 0 0 0 0 0 0 1.1920 -2.0971 -1.4657 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3296 -0.5954 -1.7733 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7044 -0.1372 -0.8568 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2906 -0.5120 1.7332 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7771 -2.3931 0.0372 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.5091 -1.1140 -1.2736 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1626 0.3566 0.2051 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.4606 3.1209 -0.8598 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.1027 5.2151 -1.2469 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.2433 3.3875 -0.1144 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.4998 -1.8872 3.3525 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9972 -3.6179 2.5349 H 0 0 0 0 0 0 0 0 0 0 0 0 1.7486 -2.8489 1.7274 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 2 3 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 7 9 2 0 9 10 1 0 10 11 1 0 11 12 2 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 0 16 17 2 0 16 18 1 0 18 19 2 0 19 20 1 0 19 21 1 0 21 22 2 0 22 23 1 0 22 24 1 0 24 25 2 0 25 26 1 0 13 27 2 0 27 28 1 0 27 29 1 0 29 30 2 0 30 31 1 0 30 11 1 0 26 14 1 0 25 18 1 0 1 32 1 0 1 33 1 0 1 34 1 0 3 35 1 0 3 36 1 0 3 37 1 0 4 38 1 0 5 39 1 0 5 40 1 0 6 41 1 0 6 42 1 0 8 43 1 0 8 44 1 0 8 45 1 0 9 46 1 0 10 47 1 0 10 48 1 0 12 49 1 0 14 50 1 1 15 51 1 0 15 52 1 0 20 53 1 0 21 54 1 0 23 55 1 0 24 56 1 0 28 57 1 0 29 58 1 0 31 59 1 0 M END

Standard InCHIKey	GJFHZVPRFLHEBR-KETROQBRSA-N
Standard InCHI	InChI=1S/C25H28O6/c1-14(2)5-4-6-15(3)7-8-16-9-18(20(28)12-19(16)27)23-13-22(30)25-21(29)10-17(26)11-24(25)31-23/h5,7,9-12,23,26-29H,4,6,8,13H2,1-3H3/b15-7+/t23-/m0/s1
SMILES	CC(C)=CCC/C(C)=C/Cc1cc([C@@H]2CC(=O)c3c(O)cc(O)cc3O2)c(O)cc1O

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
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20815207]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	bark	n.a.	PMID[21319773]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	leaf	n.a.	PMID[21319773]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[21319773]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	leaf	n.a.	PMID[22207282]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[23806866]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	root bark	University of Veterinary and Pharmaceutical Sciences Brno (UVPS Brno), Brno, Czech Republic	2011-APR	PMID[24901948]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	Konya, Turkey	2007-APR	PMID[24901948]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	leaves	Chungbuk, Korea	n.a.	PMID[25935644]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	root	n.a.	PMID[25981820]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	latex	n.a.	PMID[27294120]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	Root barks	n.a.	n.a.	PMID[3097265]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28265	Morus alba	Species	Moraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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

Activity Type	# Activity
IC50	3
Inhibition	5
Activity	2

Activity Type	# Activity
Individual protein	10

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT1464	Individual protein	Phosphodiesterase 4D	Homo sapiens	IC50	=	1260.0	nM	PMID[29291443]
NPT6571	Individual protein	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	Rattus norvegicus	Inhibition	n.a.	n.a.	%	PMID[32435418]
NPT6571	Individual protein	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	Rattus norvegicus	IC50	=	28650.0	nM	PMID[32435418]
NPT5536	Individual protein	Sarcoplasmic/endoplasmic reticulum calcium ATP-ase	Oryctolagus cuniculus	Activity	n.a.	n.a.	n.a.	PMID[32435418]
NPT5536	Individual protein	Sarcoplasmic/endoplasmic reticulum calcium ATP-ase	Oryctolagus cuniculus	IC50	=	29430.0	nM	PMID[32435418]

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 NPC610511 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	20591
0.1-0.2	25793
0.2-0.3	2769
0.3-0.4	524
0.4-0.5	131
0.5-0.6	40
0.6-0.7	6
0.7-0.8	0
0.8-0.85	1
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	NPC96408
0.803	Intermediate Similarity	NPC279650
0.7286	Intermediate Similarity	NPC58805
0.6712	Remote Similarity	NPC67396
0.6471	Remote Similarity	NPC166689
0.6364	Remote Similarity	NPC258630
0.6324	Remote Similarity	NPC109223
0.6324	Remote Similarity	NPC10937
0.6	Remote Similarity	NPC106976
0.5946	Remote Similarity	NPC290133
0.5921	Remote Similarity	NPC185276
0.5915	Remote Similarity	NPC85121
0.5857	Remote Similarity	NPC17170
0.5844	Remote Similarity	NPC74924
0.5753	Remote Similarity	NPC470890
0.5753	Remote Similarity	NPC200761
0.5733	Remote Similarity	NPC228504
0.5676	Remote Similarity	NPC24136
0.5641	Remote Similarity	NPC298692
0.5625	Remote Similarity	NPC295261
0.5625	Remote Similarity	NPC296490
0.56	Remote Similarity	NPC166934
0.5493	Remote Similarity	NPC267846
0.5455	Remote Similarity	NPC64915
0.5455	Remote Similarity	NPC213896
0.5385	Remote Similarity	NPC470328
0.5385	Remote Similarity	NPC209614
0.5385	Remote Similarity	NPC164272
0.5385	Remote Similarity	NPC470327
0.5342	Remote Similarity	NPC116513
0.5342	Remote Similarity	NPC223500
0.5325	Remote Similarity	NPC474021
0.5309	Remote Similarity	NPC24640
0.525	Remote Similarity	NPC226025
0.525	Remote Similarity	NPC278778
0.5224	Remote Similarity	NPC107586
0.5185	Remote Similarity	NPC474024
0.5185	Remote Similarity	NPC474023
0.5139	Remote Similarity	NPC324436
0.5139	Remote Similarity	NPC78
0.5125	Remote Similarity	NPC227579
0.5125	Remote Similarity	NPC214166
0.5122	Remote Similarity	NPC45849
0.5122	Remote Similarity	NPC472626
0.5122	Remote Similarity	NPC210459
0.5122	Remote Similarity	NPC195796
0.5109	Remote Similarity	NPC195136
0.5063	Remote Similarity	NPC470802
0.5062	Remote Similarity	NPC111786

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC610511 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4818
0.1-0.2	4286
0.2-0.3	41
0.3-0.4	2
0.4-0.5	3
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