NPASS Compound

Natural Product: NPC125106

Natural Product ID	NPC125106
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	OVQQPOHQLNLSCP-HHATXKITSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	CHEMBL499498
PubChem CID	25016918
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0000259] Prenol lipids [CHEMONTID:0001550] Sesquiterpenoids [CHEMONTID:0002051] Agarofurans

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 85 89 0 0 0 0 0 0 0 0999 V2000 -5.3612 2.5897 0.4583 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0873 1.8466 0.7914 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2168 2.4285 1.4892 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8544 0.5775 0.3634 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.6426 -0.1247 0.6769 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0076 -1.2109 1.6611 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6317 -2.4151 1.0339 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8416 -2.9553 -0.1409 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.6909 -3.2947 -1.3125 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6670 -2.0924 -0.3797 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8511 -2.5148 -1.5733 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5148 -2.0460 -1.0420 C 0 0 1 0 0 0 0 0 0 0 0 0 0.5255 -0.5677 -1.2182 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.7562 0.1599 -0.9653 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9507 -0.6210 -0.5632 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.9867 -0.4151 -1.6899 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5366 1.1867 0.0117 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5245 2.5219 -0.2748 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7206 2.8666 -1.4772 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3023 3.5792 0.6986 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2921 4.9179 0.3832 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0732 5.8829 1.3722 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1374 5.5258 2.6840 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1273 4.1853 3.0006 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0913 3.2296 2.0107 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5407 0.0172 -0.4162 O 0 0 0 0 0 0 0 0 0 0 0 0 2.6697 0.6203 -0.8754 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8739 0.6919 -2.0934 O 0 0 0 0 0 0 0 0 0 0 0 0 3.6195 1.1726 0.0911 C 0 0 0 0 0 0 0 0 0 0 0 0 4.7346 1.7728 -0.2821 C 0 0 0 0 0 0 0 0 0 0 0 0 5.7196 2.3423 0.6257 C 0 0 0 0 0 0 0 0 0 0 0 0 5.6172 2.3247 1.9880 C 0 0 0 0 0 0 0 0 0 0 0 0 6.6299 2.9064 2.7609 C 0 0 0 0 0 0 0 0 0 0 0 0 7.7303 3.4979 2.1804 C 0 0 0 0 0 0 0 0 0 0 0 0 7.8432 3.5210 0.8079 C 0 0 0 0 0 0 0 0 0 0 0 0 6.8437 2.9477 0.0725 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4283 -2.5042 0.3730 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3371 -1.7177 1.3274 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8455 -3.9494 0.5256 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8488 -2.2324 0.7364 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8646 -3.8889 -1.8326 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0712 -4.4587 -3.0682 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.2648 -3.7167 -4.0555 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0724 -5.9230 -3.2728 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3066 -4.1917 0.3193 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.6500 3.1799 1.3472 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.1649 1.8235 0.3197 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.2779 3.1524 -0.4700 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0082 0.5797 1.2497 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8289 -0.7609 2.3041 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.2178 -1.4377 2.4011 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.6896 -2.1654 0.7204 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.7699 -3.1652 1.8456 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.3809 -2.9054 -2.2798 H 0 0 0 0 0 0 0 0 0 0 0 0 -4.7482 -2.9867 -1.0563 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.8089 -4.4089 -1.4783 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0289 -1.9312 -2.4753 H 0 0 0 0 0 0 0 0 0 0 0 0 1.2722 -2.5388 -1.6467 H 0 0 0 0 0 0 0 0 0 0 0 0 0.9019 -0.4062 -2.2765 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.9249 0.7570 -1.9196 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.0743 0.7165 -1.7307 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5975 -0.6797 -2.6730 H 0 0 0 0 0 0 0 0 0 0 0 0 -3.9740 -0.7560 -1.4190 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4591 5.1818 -0.6507 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0698 6.9197 1.1028 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3082 6.2923 3.4538 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2939 3.9094 4.0375 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.0852 2.1926 2.3376 H 0 0 0 0 0 0 0 0 0 0 0 0 3.4271 1.1004 1.1526 H 0 0 0 0 0 0 0 0 0 0 0 0 4.8944 1.8271 -1.3544 H 0 0 0 0 0 0 0 0 0 0 0 0 4.7615 1.8651 2.4533 H 0 0 0 0 0 0 0 0 0 0 0 0 6.5538 2.8949 3.8349 H 0 0 0 0 0 0 0 0 0 0 0 0 8.5140 3.9486 2.7904 H 0 0 0 0 0 0 0 0 0 0 0 0 8.7173 3.9929 0.3930 H 0 0 0 0 0 0 0 0 0 0 0 0 6.9475 2.9732 -1.0160 H 0 0 0 0 0 0 0 0 0 0 0 0 2.3665 -1.6551 0.9793 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8707 -0.7799 1.6650 H 0 0 0 0 0 0 0 0 0 0 0 0 1.3778 -2.3573 2.2617 H 0 0 0 0 0 0 0 0 0 0 0 0 1.9002 -4.0291 0.9271 H 0 0 0 0 0 0 0 0 0 0 0 0 0.8435 -4.5327 -0.3911 H 0 0 0 0 0 0 0 0 0 0 0 0 0.2283 -4.4035 1.3515 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.3163 -6.2373 -4.0246 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.8973 -6.4708 -2.3251 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.0608 -6.2808 -3.6611 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.3689 -4.8908 -0.3543 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 0 2 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 7 8 1 0 8 9 1 0 8 10 1 0 10 11 1 0 11 12 1 0 12 13 1 0 13 14 1 0 14 15 1 0 15 16 1 6 14 17 1 0 17 18 1 0 18 19 2 0 18 20 1 0 20 21 2 0 21 22 1 0 22 23 2 0 23 24 1 0 24 25 2 0 13 26 1 0 26 27 1 0 27 28 2 0 27 29 1 0 29 30 2 0 30 31 1 0 31 32 2 0 32 33 1 0 33 34 2 0 34 35 1 0 35 36 2 0 12 37 1 0 37 38 1 0 37 39 1 0 37 40 1 0 11 41 1 0 41 42 1 0 42 43 2 0 42 44 1 0 8 45 1 1 15 5 1 0 25 20 1 0 36 31 1 0 15 10 1 0 10 40 1 1 1 46 1 0 1 47 1 0 1 48 1 0 5 49 1 1 6 50 1 0 6 51 1 0 7 52 1 0 7 53 1 0 9 54 1 0 9 55 1 0 9 56 1 0 11 57 1 6 12 58 1 6 13 59 1 6 14 60 1 6 16 61 1 0 16 62 1 0 16 63 1 0 21 64 1 0 22 65 1 0 23 66 1 0 24 67 1 0 25 68 1 0 29 69 1 0 30 70 1 0 32 71 1 0 33 72 1 0 34 73 1 0 35 74 1 0 36 75 1 0 38 76 1 0 38 77 1 0 38 78 1 0 39 79 1 0 39 80 1 0 39 81 1 0 44 82 1 0 44 83 1 0 44 84 1 0 45 85 1 0 M END

Standard InCHIKey	OVQQPOHQLNLSCP-HHATXKITSA-N
Standard InCHI	InChI=1S/C35H40O10/c1-21(36)41-25-19-20-33(5,40)35-29(42-22(2)37)27(32(3,4)45-35)28(43-26(38)18-17-23-13-9-7-10-14-23)30(34(25,35)6)44-31(39)24-15-11-8-12-16-24/h7-18,25,27-30,40H,19-20H2,1-6H3/b18-17+/t25-,27+,28-,29+,30-,33-,34-,35-/m0/s1
SMILES	CC(=O)O[C@H]1CC[C@@](C)([C@@]23[C@@H]([C@@H]([C@@H]([C@@H]([C@]12C)OC(=O)c1ccccc1)OC(=O)/C=C/c1ccccc1)C(C)(C)O3)OC(=O)C)O

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
NPO15653	Celastrus vulcanicola	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18616221]
NPO15653	Celastrus vulcanicola	Species	Celastraceae	Eukaryota	stems	Montecristo National Park, province of Santa Ana, El Salvador	2004-JUN	PMID[20873773]
NPO15653	Celastrus vulcanicola	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21419633]
NPO15653	Celastrus vulcanicola	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25695368]
NPO15653	Celastrus vulcanicola	Species	Celastraceae	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
Ki	1
Activity	1
MIC	2

Activity Type	# Activity
Individual protein	2
Organism	2

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	Ki	=	290.0	nM	PMID[22245048]
NPT668	Individual protein	P-glycoprotein 1	Homo sapiens	Activity	=	83.0	%	PMID[21420296]

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	MIC	=	12.5	ug.mL-1	PMID[17883259]
NPT790	Organism	Mycobacterium tuberculosis H37Rv	Mycobacterium tuberculosis H37Rv	MIC	>	25.0	ug.mL-1	PubChem BioAssay data set

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 NPC125106 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	10795
0.1-0.2	35381
0.2-0.3	2951
0.3-0.4	535
0.4-0.5	132
0.5-0.6	43
0.6-0.7	13
0.7-0.8	0
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	NPC472573
0.7639	Intermediate Similarity	NPC163719
0.7639	Intermediate Similarity	NPC95810
0.7125	Intermediate Similarity	NPC70403
0.7125	Intermediate Similarity	NPC177940
0.6548	Remote Similarity	NPC301368
0.6548	Remote Similarity	NPC84815
0.6386	Remote Similarity	NPC603877
0.6375	Remote Similarity	NPC57628
0.6322	Remote Similarity	NPC253738
0.6304	Remote Similarity	NPC6981
0.6265	Remote Similarity	NPC29704
0.6265	Remote Similarity	NPC470157
0.6163	Remote Similarity	NPC188865
0.6163	Remote Similarity	NPC184817
0.6154	Remote Similarity	NPC483886
0.6145	Remote Similarity	NPC481050
0.6	Remote Similarity	NPC470159
0.5952	Remote Similarity	NPC609221
0.5949	Remote Similarity	NPC281717
0.5875	Remote Similarity	NPC291599
0.5875	Remote Similarity	NPC200471
0.5875	Remote Similarity	NPC472575
0.5862	Remote Similarity	NPC610927
0.5814	Remote Similarity	NPC472571
0.5775	Remote Similarity	NPC470154
0.5699	Remote Similarity	NPC476975
0.5647	Remote Similarity	NPC476970
0.5604	Remote Similarity	NPC476974
0.557	Remote Similarity	NPC66761
0.557	Remote Similarity	NPC483843
0.5567	Remote Similarity	NPC483880
0.5567	Remote Similarity	NPC156941
0.5556	Remote Similarity	NPC87448
0.5529	Remote Similarity	NPC210591
0.5506	Remote Similarity	NPC483865
0.5455	Remote Similarity	NPC488917
0.5455	Remote Similarity	NPC483878
0.5455	Remote Similarity	NPC476971
0.5444	Remote Similarity	NPC483859
0.5417	Remote Similarity	NPC471980
0.5375	Remote Similarity	NPC211137
0.5341	Remote Similarity	NPC481486
0.5287	Remote Similarity	NPC473085
0.5287	Remote Similarity	NPC473112
0.5233	Remote Similarity	NPC472569
0.5233	Remote Similarity	NPC16912
0.5227	Remote Similarity	NPC470153
0.5227	Remote Similarity	NPC481489
0.5222	Remote Similarity	NPC25768
0.5185	Remote Similarity	NPC476094
0.5176	Remote Similarity	NPC471104
0.5176	Remote Similarity	NPC171207
0.5169	Remote Similarity	NPC481488
0.5165	Remote Similarity	NPC174982
0.5114	Remote Similarity	NPC607428
0.5109	Remote Similarity	NPC171525
0.5059	Remote Similarity	NPC472572
0.5057	Remote Similarity	NPC11685
0.5055	Remote Similarity	NPC483866
0.5053	Remote Similarity	NPC476973

Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC125106 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4167
0.1-0.2	4866
0.2-0.3	117
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