NPASS Compound

Structure

NPC289274 OpenBabel06302215382D 73 79 0 0 1 0 0 0 0 0999 V2000 -3.6036 0.1194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9344 -0.6237 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.9563 -0.4158 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.2872 -1.1590 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5962 -2.1100 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5743 -2.3179 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.2435 -1.5748 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8833 -3.2690 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.8615 -3.4769 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.5306 -2.7338 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.5088 -2.9417 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.8178 -3.8927 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7959 -4.1006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4651 -3.3575 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.4432 -3.5654 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.7522 -4.5165 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.1123 -2.8223 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.8033 -1.8712 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.8523 -1.5622 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.8523 -0.5622 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -7.0433 0.0256 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1297 -0.3811 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.8033 -0.2532 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.3911 -1.0622 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.2571 -1.5622 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.2571 -2.5622 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.2571 -0.5622 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.2571 0.4378 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -9.3911 0.9378 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -9.3911 1.9378 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -10.2571 2.4378 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.1232 1.9378 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -11.9892 2.4378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.8552 1.9378 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.7212 2.4378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -14.5873 1.9378 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -13.7212 3.4378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.8552 3.9378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -12.8552 4.9378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -13.7212 5.4378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -14.5873 4.9378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -14.5873 3.9378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.1232 0.9378 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -10.2571 3.4378 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.1232 3.9378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.9892 3.4378 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -11.1232 4.9378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.2571 5.4378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -10.2571 6.4378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.1232 6.9378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.9892 6.4378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -11.9892 5.4378 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.5251 2.4378 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -8.5251 0.4378 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.0433 -2.1500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1487 -4.6359 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1705 -4.4280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.5014 -5.1711 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5232 -4.9632 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9271 -2.8532 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3090 -0.9511 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6473 0.5352 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.6691 0.7431 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.3601 1.6942 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.6180 1.9021 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.2872 1.1590 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.9781 0.2079 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6473 -0.5352 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6254 -0.3273 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.2653 1.3669 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9271 2.8532 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.0292 2.4373 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 1 0 0 0 2 3 1 0 0 0 0 2 7 1 0 0 0 0 3 4 1 0 0 0 0 3 62 1 6 0 0 0 4 5 1 0 0 0 0 4 61 1 1 0 0 0 5 6 1 0 0 0 0 5 60 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 6 0 0 0 8 9 1 0 0 0 0 9 57 2 0 0 0 0 9 10 1 0 0 0 0 10 11 2 0 0 0 0 11 12 1 0 0 0 0 12 13 1 0 0 0 0 12 56 2 0 0 0 0 13 14 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 18 17 1 6 0 0 0 18 19 1 0 0 0 0 18 24 1 0 0 0 0 19 20 1 0 0 0 0 19 55 1 1 0 0 0 20 21 1 6 0 0 0 20 23 1 0 0 0 0 21 22 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 1 0 0 0 24 27 1 0 0 0 0 25 26 1 0 0 0 0 28 27 1 1 0 0 0 28 29 1 0 0 0 0 28 43 1 0 0 0 0 29 30 1 0 0 0 0 29 54 1 1 0 0 0 30 31 1 0 0 0 0 30 53 1 6 0 0 0 31 32 1 0 0 0 0 31 44 1 1 0 0 0 32 33 1 6 0 0 0 32 43 1 0 0 0 0 33 34 1 0 0 0 0 34 35 1 0 0 0 0 35 36 2 0 0 0 0 35 37 1 0 0 0 0 37 42 2 0 0 0 0 37 38 1 0 0 0 0 38 39 2 0 0 0 0 39 40 1 0 0 0 0 40 41 2 0 0 0 0 41 42 1 0 0 0 0 44 45 1 0 0 0 0 45 46 2 0 0 0 0 45 47 1 0 0 0 0 47 52 2 0 0 0 0 47 48 1 0 0 0 0 48 49 2 0 0 0 0 49 50 1 0 0 0 0 50 51 2 0 0 0 0 51 52 1 0 0 0 0 56 57 1 0 0 0 0 57 58 1 0 0 0 0 58 59 1 0 0 0 0 63 62 1 1 0 0 0 63 64 1 0 0 0 0 63 70 1 0 0 0 0 64 65 1 0 0 0 0 64 73 1 6 0 0 0 65 66 1 0 0 0 0 65 72 1 1 0 0 0 66 67 1 0 0 0 0 66 71 1 6 0 0 0 67 68 1 1 0 0 0 67 70 1 0 0 0 0 68 69 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	1034.33
Volume:	964.35
LogP:	1.037
LogD:	0.273
LogS:	-2.8
# Rotatable Bonds:	21
TPSA:	375.27
# H-Bond Aceptor:	25
# H-Bond Donor:	11
# Rings:	7
# Heavy Atoms:	25

MedChem Properties

QED Drug-Likeness Score:	0.034
Synthetic Accessibility Score:	6.026
Fsp3:	0.521
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.531
MDCK Permeability:	0.00017377454787492752
Pgp-inhibitor:	0.003
Pgp-substrate:	0.998
Human Intestinal Absorption (HIA):	0.99
20% Bioavailability (F20%):	0.009
30% Bioavailability (F30%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.101
Plasma Protein Binding (PPB):	63.57014083862305%
Volume Distribution (VD):	0.334
Pgp-substrate:	7.645181655883789%

ADMET: Metabolism

CYP1A2-inhibitor:	0.019
CYP1A2-substrate:	0.006
CYP2C19-inhibitor:	0.011
CYP2C19-substrate:	0.057
CYP2C9-inhibitor:	0.003
CYP2C9-substrate:	0.037
CYP2D6-inhibitor:	0.008
CYP2D6-substrate:	0.059
CYP3A4-inhibitor:	0.06
CYP3A4-substrate:	0.013

ADMET: Excretion

Clearance (CL):	1.124
Half-life (T1/2):	0.707

ADMET: Toxicity

hERG Blockers:	0.62
Human Hepatotoxicity (H-HT):	0.04
Drug-inuced Liver Injury (DILI):	0.976
AMES Toxicity:	0.088
Rat Oral Acute Toxicity:	0.0
Maximum Recommended Daily Dose:	0.0
Skin Sensitization:	0.628
Carcinogencity:	0.031
Eye Corrosion:	0.003
Eye Irritation:	0.02
Respiratory Toxicity:	0.001

Download Data

Data Type	Select
General Info & Identifiers & Properties
Structure MOL file
Source Organisms
Biological Activities
Similar NPs/Drugs

Natural Product: NPC289274

Natural Product ID:	NPC289274
*Common Name:**	ADMVOMDWHCGMPZ-KVTKYYLJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	ADMVOMDWHCGMPZ-KVTKYYLJSA-N
Standard InCHI:	InChI=1S/C48H58O25/c1-22-40(71-46-37(58)34(55)32(53)28(18-49)67-46)35(56)38(59)45(65-22)66-26-15-13-23(17-27(26)63-2)14-16-31(52)69-42-33(54)29(19-50)72-48(42,21-51)73-47-39(60)36(57)41(70-44(62)25-11-7-4-8-12-25)30(68-47)20-64-43(61)24-9-5-3-6-10-24/h3-17,22,28-30,32-42,45-47,49-51,53-60H,18-21H2,1-2H3/b16-14+/t22-,28+,29+,30+,32+,33+,34-,35-,36+,37+,38+,39+,40-,41+,42-,45-,46-,47+,48-/m0/s1
SMILES:	C[C@H]1[C@@H]([C@H]([C@H]([C@@H](O1)Oc1ccc(/C=C/C(=O)O[C@H]2[C@@H]([C@@H](CO)O[C@@]2(CO)O[C@@H]2[C@@H]([C@H]([C@@H]([C@@H](COC(=O)c3ccccc3)O2)OC(=O)c2ccccc2)O)O)O)cc1OC)O)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	101707478
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates [CHEMONTID:0002105] Glycosyl compounds [CHEMONTID:0004165] Phenolic glycosides

*Note: the InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.
**Note: the Chemical Classification was calculated by NPClassifier Version 1.5. Reference: PMID:34662515.

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO28551	Centaurium erythraea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1021/np50044a037]
NPO28776	Casearia arborea	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[10843580]
NPO28166	Streptomyces nodosus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[15730252]
NPO22789	Ecklonia cava	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18693022]
NPO22789	Ecklonia cava	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19201199]
NPO22789	Ecklonia cava	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23647823]
NPO28205	Isodon setschwanensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28365	Gelasinospora kobi	Species	Sordariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28166	Streptomyces nodosus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO28776	Casearia arborea	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28434	Isotropis forrestii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24709	Justicia tranquebariensis	Species	Acanthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28659	Euphorbia terracina	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28456	Anaptychia obscurata	Species	Physciaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28205	Isodon setschwanensis	Species	Lamiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO25755	Haplopappus multifolius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28515	Campanula kachetica	Species	Campanulaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14228	Mattfeldanthus nobilis	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO28551	Centaurium erythraea	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO22789	Ecklonia cava	Species	Lessoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28239	Indigofera hirsuta	Species	Fabaceae	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	NP ID	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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ Note for Activity Records:
☉ The quantitative biological activities were primarily integrated from ChEMBL (Version-30) database and were also directly collected from PubMed literature. PubMed PMID was provided as the reference link for each activity record.

Chemically structural similarity: I. Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes 4,3285 NPs with experimentally-derived bioactivity available in NPASS)

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules. Tc lies between [0, 1] where '1' indicates the highest similarity. What is Tanimoto coefficient

● The left chart: Distribution of similarity level between NPC289274 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	346
0.1-0.2	1435
0.2-0.3	3186
0.3-0.4	7389
0.4-0.5	10102
0.5-0.6	6909
0.6-0.7	8505
0.7-0.8	4184
0.8-0.85	554
0.85-0.9	84
0.9-0.95	3
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID

Chemically structural similarity: II. Similar Clinical/Approved Drugs

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

● The left chart: Distribution of similarity level between NPC289274 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	287
0.1-0.2	801
0.2-0.3	1706
0.3-0.4	2658
0.4-0.5	2138
0.5-0.6	1065
0.6-0.7	425
0.7-0.8	59
0.8-0.85	11
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage

Bioactivity similarity: Similar Natural Products in NPASS

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