NPASS Compound

Structure

NPC267026 OpenBabel06302215232D 37 40 0 0 1 0 0 0 0 0999 V2000 4.3776 -1.4067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3776 -0.4067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.5116 0.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6456 -0.4067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7796 0.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7796 1.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6456 1.5933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5116 1.0933 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3776 1.5933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2437 1.0933 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.1097 1.5933 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.9757 1.0933 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 6.9757 0.0933 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.1097 -0.4067 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.1097 -1.4067 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.9757 -1.9067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.2437 0.0933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.8417 -0.4067 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.8417 1.5933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.1097 2.5933 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9135 -0.4067 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.8090 -1.4013 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.5522 -2.0704 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5032 -1.7614 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1691 -1.6092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6691 -2.4752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6691 -2.4752 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.1691 -3.3412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1691 -3.3412 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.6691 -4.2072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1691 -5.0733 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1691 -1.6092 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6691 -0.7431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6691 -0.7431 0.0000 C 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 -2.1691 0.1229 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6691 0.9889 0.0000 C 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 6 7 2 0 0 0 0 7 8 1 0 0 0 0 8 9 1 0 0 0 0 10 9 1 1 0 0 0 10 11 1 0 0 0 0 10 17 1 0 0 0 0 11 12 1 0 0 0 0 11 20 1 6 0 0 0 12 13 1 0 0 0 0 12 19 1 1 0 0 0 13 14 1 0 0 0 0 13 18 1 6 0 0 0 14 15 1 1 0 0 0 14 17 1 0 0 0 0 15 16 1 0 0 0 0 21 5 1 1 0 0 0 21 22 1 0 0 0 0 21 35 1 0 0 0 0 22 23 1 6 0 0 0 22 25 1 0 0 0 0 23 24 1 0 0 0 0 25 34 2 0 0 0 0 25 26 1 0 0 0 0 26 27 2 0 0 0 0 27 28 1 0 0 0 0 27 32 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 30 31 1 0 0 0 0 32 33 2 0 0 0 0 33 34 1 0 0 0 0 33 36 1 0 0 0 0 34 35 1 0 0 0 0 36 37 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	520.19
Volume:	502.264
LogP:	0.591
LogD:	0.561
LogS:	-3.59
# Rotatable Bonds:	9
TPSA:	167.53
# H-Bond Aceptor:	11
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.265
Synthetic Accessibility Score:	4.371
Fsp3:	0.462
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.893
MDCK Permeability:	2.572376797616016e-05
Pgp-inhibitor:	0.013
Pgp-substrate:	0.975
Human Intestinal Absorption (HIA):	0.565
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.717

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.379
Plasma Protein Binding (PPB):	49.99517059326172%
Volume Distribution (VD):	0.34
Pgp-substrate:	22.284183502197266%

ADMET: Metabolism

CYP1A2-inhibitor:	0.019
CYP1A2-substrate:	0.181
CYP2C19-inhibitor:	0.008
CYP2C19-substrate:	0.797
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.396
CYP2D6-inhibitor:	0.001
CYP2D6-substrate:	0.203
CYP3A4-inhibitor:	0.034
CYP3A4-substrate:	0.42

ADMET: Excretion

Clearance (CL):	2.588
Half-life (T1/2):	0.607

ADMET: Toxicity

hERG Blockers:	0.233
Human Hepatotoxicity (H-HT):	0.431
Drug-inuced Liver Injury (DILI):	0.651
AMES Toxicity:	0.448
Rat Oral Acute Toxicity:	0.042
Maximum Recommended Daily Dose:	0.038
Skin Sensitization:	0.287
Carcinogencity:	0.63
Eye Corrosion:	0.003
Eye Irritation:	0.01
Respiratory Toxicity:	0.008

Download Data

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

Natural Product: NPC267026

Natural Product ID:	NPC267026
*Common Name:**	SPWHQAUMLDQOFU-AQRJENMISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	SPWHQAUMLDQOFU-AQRJENMISA-N
Standard InCHI:	InChI=1S/C26H32O11/c1-33-18-10-14(5-6-17(18)35-26-23(32)22(31)21(30)20(12-29)36-26)24-16(11-28)15-8-13(4-3-7-27)9-19(34-2)25(15)37-24/h3-6,8-10,16,20-24,26-32H,7,11-12H2,1-2H3/b4-3+/t16-,20-,21-,22+,23-,24+,26-/m1/s1
SMILES:	COc1cc(ccc1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)[C@H]1[C@H](CO)c2cc(/C=C/CO)cc(c2O1)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	66552022
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0003405] 2-arylbenzofuran flavonoids

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO27523	Brickellia glutinosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6436442]
NPO27022	Neisseria meningitidis	Species	Neisseriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[4990768]
NPO27759	Fusarium poae	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25475336]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	aerial part	n.a.	n.a.	PMID[25442304]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20038159]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	Whole plant	n.a.	n.a.	PMID[16643038]
NPO27416	Ceratonia siliqua	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27536	Sidastrum quinquenervium	Species	Malvaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8618	Hypotrachyna cirrhata	Species	Parmeliaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27177	Telitoxicum glaziovii	Species	Menispermaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
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☑ 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 NPC267026 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	414
0.1-0.2	1455
0.2-0.3	3594
0.3-0.4	9150
0.4-0.5	9343
0.5-0.6	4804
0.6-0.7	8298
0.7-0.8	4448
0.8-0.85	799
0.85-0.9	330
0.9-0.95	44
0.95-1	18

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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 NPC267026 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	337
0.1-0.2	805
0.2-0.3	1700
0.3-0.4	2778
0.4-0.5	1782
0.5-0.6	1010
0.6-0.7	617
0.7-0.8	113
0.8-0.85	7
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
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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