NPASS Compound

Structure

NPC100720 OpenBabel06302215202D 32 35 0 0 1 0 0 0 0 0999 V2000 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 O 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 0 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 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3301 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 O 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 3.4641 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 2.0000 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 6.0622 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 2.0000 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 7.7942 3.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 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 -1.7321 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 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 -0.8660 1.5000 0.0000 C 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 0.0000 0.0000 O 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 -2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 1 0 0 0 0 3 8 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 21 1 0 0 0 0 6 7 2 0 0 0 0 7 13 1 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 9 10 2 0 0 0 0 9 11 1 0 0 0 0 11 12 2 0 0 0 0 11 14 1 0 0 0 0 12 13 1 0 0 0 0 14 19 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 20 1 0 0 0 0 18 19 1 0 0 0 0 22 21 1 1 0 0 0 22 23 1 0 0 0 0 22 29 1 0 0 0 0 23 24 1 0 0 0 0 23 32 1 6 0 0 0 24 25 1 0 0 0 0 24 31 1 1 0 0 0 25 26 1 0 0 0 0 25 30 1 6 0 0 0 26 27 1 1 0 0 0 26 29 1 0 0 0 0 27 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	446.12
Volume:	421.653
LogP:	0.876
LogD:	1.385
LogS:	-3.881
# Rotatable Bonds:	5
TPSA:	159.05
# H-Bond Aceptor:	10
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	10

MedChem Properties

QED Drug-Likeness Score:	0.37
Synthetic Accessibility Score:	3.805
Fsp3:	0.318
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.185
MDCK Permeability:	1.8473232557880692e-05
Pgp-inhibitor:	0.009
Pgp-substrate:	0.483
Human Intestinal Absorption (HIA):	0.308
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.906

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.088
Plasma Protein Binding (PPB):	84.9910659790039%
Volume Distribution (VD):	0.737
Pgp-substrate:	9.636895179748535%

ADMET: Metabolism

CYP1A2-inhibitor:	0.135
CYP1A2-substrate:	0.1
CYP2C19-inhibitor:	0.043
CYP2C19-substrate:	0.067
CYP2C9-inhibitor:	0.043
CYP2C9-substrate:	0.651
CYP2D6-inhibitor:	0.487
CYP2D6-substrate:	0.488
CYP3A4-inhibitor:	0.075
CYP3A4-substrate:	0.049

ADMET: Excretion

Clearance (CL):	4.736
Half-life (T1/2):	0.675

ADMET: Toxicity

hERG Blockers:	0.197
Human Hepatotoxicity (H-HT):	0.066
Drug-inuced Liver Injury (DILI):	0.436
AMES Toxicity:	0.413
Rat Oral Acute Toxicity:	0.049
Maximum Recommended Daily Dose:	0.01
Skin Sensitization:	0.381
Carcinogencity:	0.354
Eye Corrosion:	0.003
Eye Irritation:	0.118
Respiratory Toxicity:	0.028

Download Data

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

Natural Product: NPC100720

Natural Product ID:	NPC100720
*Common Name:**	KSVVGBSBNPMXJF-RECXWPGBSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	KSVVGBSBNPMXJF-RECXWPGBSA-N
Standard InCHI:	InChI=1S/C22H22O10/c1-29-14-6-12(31-22-21(28)20(27)19(26)16(8-23)32-22)7-15-17(14)18(25)13(9-30-15)10-2-4-11(24)5-3-10/h2-7,9,16,19-24,26-28H,8H2,1H3/t16-,19-,20+,21-,22-/m1/s1
SMILES:	COc1cc(cc2c1c(=O)c(co2)c1ccc(cc1)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:	189922
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0000507] Isoflavonoid O-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
NPO24639	Streptomyces filamentosus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	PMID[17284073]
NPO546	Candida albicans	Species	Debaryomycetaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23902158]
NPO16444	Apios americana	Species	Fabaceae	Eukaryota	Tubers	n.a.	n.a.	PMID[29932657]
NPO11127	Inulanthera calva	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO24639	Streptomyces filamentosus	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO15875	Scolopia chinensis	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO7011	Chamomilla recutita	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO4061	Trollius europaeus	Species	Ranunculaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO26656	Heliotropium hirsutissimum	Species	Heliotropiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO546	Candida albicans	Species	Debaryomycetaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO12152	Nicotiana raimondii	Species	Solanaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9830	Arum maximum	Species	Araceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO16444	Apios americana	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

Activity Type	# Activity
IC50	1

Activity Type	# Activity
Cell Line	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT113	Cell Line	RAW264.7	Mus musculus	IC50	>	1000.0	nM	PMID[29932657]

☑ 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 NPC100720 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	398
0.1-0.2	1673
0.2-0.3	3552
0.3-0.4	8978
0.4-0.5	9538
0.5-0.6	4372
0.6-0.7	5553
0.7-0.8	4992
0.8-0.85	2509
0.85-0.9	815
0.9-0.95	281
0.95-1	36

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 NPC100720 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	368
0.1-0.2	904
0.2-0.3	1737
0.3-0.4	2676
0.4-0.5	1940
0.5-0.6	1038
0.6-0.7	306
0.7-0.8	131
0.8-0.85	35
0.85-0.9	12
0.9-0.95	2
0.95-1	1

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