NPASS Compound

Structure

NPC244229 OpenBabel06302216202D 31 33 0 0 1 0 0 0 0 0999 V2000 -0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 1.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -2.5981 2.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 2.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.7321 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 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 1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2 1 1 6 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 31 1 1 0 0 0 4 5 1 0 0 0 0 4 19 1 6 0 0 0 5 6 1 0 0 0 0 5 18 1 1 0 0 0 6 7 1 0 0 0 0 6 8 1 1 0 0 0 8 9 1 0 0 0 0 9 14 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 2 0 0 0 0 12 15 1 0 0 0 0 13 14 1 0 0 0 0 15 16 1 0 0 0 0 16 17 3 0 0 0 0 20 19 1 6 0 0 0 20 21 1 0 0 0 0 20 27 1 0 0 0 0 21 22 1 0 0 0 0 21 30 1 1 0 0 0 22 23 1 0 0 0 0 22 29 1 6 0 0 0 23 24 1 0 0 0 0 23 28 1 1 0 0 0 24 25 1 6 0 0 0 24 27 1 0 0 0 0 25 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	284.1
Volume:	293.625
LogP:	3.687
LogD:	3.072
LogS:	-4.424
# Rotatable Bonds:	2
TPSA:	55.76
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	3
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.918
Synthetic Accessibility Score:	2.716
Fsp3:	0.235
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.718
MDCK Permeability:	1.5153947970247827e-05
Pgp-inhibitor:	0.076
Pgp-substrate:	0.001
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.001
30% Bioavailability (F30%):	0.004

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.579
Plasma Protein Binding (PPB):	97.4140853881836%
Volume Distribution (VD):	0.524
Pgp-substrate:	1.4014092683792114%

ADMET: Metabolism

CYP1A2-inhibitor:	0.682
CYP1A2-substrate:	0.857
CYP2C19-inhibitor:	0.95
CYP2C19-substrate:	0.707
CYP2C9-inhibitor:	0.901
CYP2C9-substrate:	0.888
CYP2D6-inhibitor:	0.573
CYP2D6-substrate:	0.709
CYP3A4-inhibitor:	0.599
CYP3A4-substrate:	0.343

ADMET: Excretion

Clearance (CL):	7.515
Half-life (T1/2):	0.214

ADMET: Toxicity

hERG Blockers:	0.034
Human Hepatotoxicity (H-HT):	0.735
Drug-inuced Liver Injury (DILI):	0.907
AMES Toxicity:	0.288
Rat Oral Acute Toxicity:	0.808
Maximum Recommended Daily Dose:	0.617
Skin Sensitization:	0.431
Carcinogencity:	0.659
Eye Corrosion:	0.004
Eye Irritation:	0.887
Respiratory Toxicity:	0.902

Download Data

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

Natural Product: NPC244229

Natural Product ID:	NPC244229
*Common Name:**	CKIYKMQZQIRHJO-CNTWJFQTSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	CKIYKMQZQIRHJO-CNTWJFQTSA-N
Standard InCHI:	InChI=1S/C20H27NO10/c1-9-13(23)18(31-19-16(26)15(25)14(24)12(8-22)30-19)17(27)20(28-9)29-11-4-2-10(3-5-11)6-7-21/h2-5,9,12-20,22-27H,6,8H2,1H3/t9-,12-,13-,14-,15+,16-,17-,18+,19+,20-/m1/s1
SMILES:	C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)Oc1ccc(cc1)CC#N)O)O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	11419325
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
NPO681	Mesua ferrea	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	DOI[10.1016/S0040-4020(01)83306-8]
NPO4410	Laggera alata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[12932128]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	n.a.	leaf	n.a.	PMID[24024688]
NPO3302	Fusarium avenaceum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25475336]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[7798960]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	Shoot	n.a.	n.a.	Database[FooDB]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO681	Mesua ferrea	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6187	Sequoia sempervirens	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO5536	Papaver persicum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO495	Daemonorops draco	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6187	Sequoia sempervirens	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO495	Daemonorops draco	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO5536	Papaver persicum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3905	Medinilla magnifica	Species	Melastomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4410	Laggera alata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO681	Mesua ferrea	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO495	Daemonorops draco	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO5536	Papaver persicum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO495	Daemonorops draco	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO5937	Garrya laurifolia	Species	Garryaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2703	Petteria ramentacea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4858	Helipterum gnaphaloides	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5021	Podospora curvicolla	Species	Lasiosphaeriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO823	Senecio cathcartensis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8703	Monopteryx uaucu	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5536	Papaver persicum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO495	Daemonorops draco	Species	Arecaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3905	Medinilla magnifica	Species	Melastomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4221	Fusarium sacchari	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6187	Sequoia sempervirens	Species	Cupressaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7963	Excoecaria acerifolia	Species	Euphorbiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO681	Mesua ferrea	Species	Calophyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4410	Laggera alata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8339	Lithothamnion corallioides	Species	Hapalidiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3302	Fusarium avenaceum	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1585	Onobrychis bobrovii	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7266	Goupia glabra	Species	Goupiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11021	Moringa oleifera	Species	Moringaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO2501	Trifolium strepens	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 NPC244229 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	250
0.1-0.2	1373
0.2-0.3	4083
0.3-0.4	11369
0.4-0.5	7759
0.5-0.6	9026
0.6-0.7	7186
0.7-0.8	1464
0.8-0.85	164
0.85-0.9	21
0.9-0.95	1
0.95-1	1

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 NPC244229 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	196
0.1-0.2	805
0.2-0.3	1552
0.3-0.4	2896
0.4-0.5	1942
0.5-0.6	1156
0.6-0.7	550
0.7-0.8	52
0.8-0.85	1
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