NPASS Compound

Structure

CID113550 OpenBabel06191715462D 30 35 0 0 1 0 0 0 0 0999 V2000 -2.6492 0.7745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6856 -0.1809 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5969 5.5183 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3929 -0.0025 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4710 3.7194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.9056 2.7488 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6608 0.9975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7948 2.4975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6315 4.6993 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.8633 4.0801 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6883 1.0516 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9081 2.8200 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7948 1.4975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.0314 4.5476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5269 1.4975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4660 3.5770 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.6608 2.9975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.3477 1.9918 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.0289 4.4764 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5269 2.4975 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8994 0.4371 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.0712 0.9975 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.5944 5.4471 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.3929 0.9975 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4564 3.7147 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.8687 3.9756 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7493 5.1700 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.2700 3.1666 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.3483 1.9583 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 11 1 0 0 0 0 2 21 1 0 0 0 0 3 23 1 0 0 0 0 4 24 1 0 0 0 0 5 12 2 0 0 0 0 5 14 1 0 0 0 0 6 12 1 0 0 0 0 6 16 2 0 0 0 0 7 13 2 0 0 0 0 7 15 1 0 0 0 0 8 13 1 0 0 0 0 8 17 2 0 0 0 0 9 25 1 0 0 0 0 9 27 1 0 0 0 0 10 26 1 0 0 0 0 10 28 1 0 0 0 0 11 18 1 0 0 0 0 11 21 1 6 0 0 0 14 19 2 0 0 0 0 14 23 1 0 0 0 0 15 20 2 0 0 0 0 15 24 1 0 0 0 0 16 19 1 0 0 0 0 16 25 1 0 0 0 0 17 20 1 0 0 0 0 17 26 1 0 0 0 0 18 12 1 1 0 0 0 18 29 1 0 0 0 0 19 27 1 0 0 0 0 20 28 1 0 0 0 0 21 22 1 6 0 0 0 21 30 1 0 0 0 0 22 13 1 6 0 0 0 22 29 1 0 0 0 0 22 30 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	414.13
Volume:	392.232
LogP:	3.977
LogD:	3.592
LogS:	-6.1
# Rotatable Bonds:	4
TPSA:	77.14
# H-Bond Aceptor:	8
# H-Bond Donor:	0
# Rings:	6
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.704
Synthetic Accessibility Score:	4.32
Fsp3:	0.455
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.813
MDCK Permeability:	5.8412937505636364e-05
Pgp-inhibitor:	0.964
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.001
20% Bioavailability (F20%):	0.003
30% Bioavailability (F30%):	0.02

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.121
Plasma Protein Binding (PPB):	87.99678802490234%
Volume Distribution (VD):	0.952
Pgp-substrate:	6.135263442993164%

ADMET: Metabolism

CYP1A2-inhibitor:	0.313
CYP1A2-substrate:	0.981
CYP2C19-inhibitor:	0.92
CYP2C19-substrate:	0.895
CYP2C9-inhibitor:	0.591
CYP2C9-substrate:	0.602
CYP2D6-inhibitor:	0.888
CYP2D6-substrate:	0.899
CYP3A4-inhibitor:	0.973
CYP3A4-substrate:	0.916

ADMET: Excretion

Clearance (CL):	15.351
Half-life (T1/2):	0.194

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.614
Drug-inuced Liver Injury (DILI):	0.747
AMES Toxicity:	0.431
Rat Oral Acute Toxicity:	0.031
Maximum Recommended Daily Dose:	0.861
Skin Sensitization:	0.88
Carcinogencity:	0.976
Eye Corrosion:	0.003
Eye Irritation:	0.329
Respiratory Toxicity:	0.932

Download Data

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

Natural Product: NPC113550

Natural Product ID:	NPC113550
*Common Name:**	Beilschmin D
IUPAC Name:	4-methoxy-6-[(1S,3S,4R,5S)-1-(7-methoxy-1,3-benzodioxol-5-yl)-4,5-dimethyl-2,6-dioxabicyclo[3.1.0]hexan-3-yl]-1,3-benzodioxole
Synonyms:	Beilschmin D
Standard InCHIKey:	CVGWCATWCAZNFN-YMIXRQRSSA-N
Standard InCHI:	InChI=1S/C22H22O8/c1-11-18(12-5-14(23-3)19-16(6-12)25-9-27-19)29-22(21(11,2)30-22)13-7-15(24-4)20-17(8-13)26-10-28-20/h5-8,11,18H,9-10H2,1-4H3/t11-,18+,21+,22+/m1/s1
SMILES:	COc1cc(cc2c1OCO2)[C@H]1O[C@@]2([C@]([C@@H]1C)(O2)C)c1cc(OC)c2c(c1)OCO2
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2204390
PubChem CID:	71455792
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001969] Dibenzylbutane lignans

*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
NPO4331	Plakortis lita	Species	Plakinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[9722494]
NPO2861	Pentaceraster regulus	Species	n.a.	n.a.	n.a.	n.a.	n.a.	PMID[28981263]
NPO8247	Austrobaileya scandens	Species	Austrobaileyaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27214307]
NPO25126	Sarcophyton latum	Species	Orchidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[16724849]
NPO25126	Sarcophyton latum	Species	Orchidaceae	Eukaryota	n.a.	Hainan soft coral	n.a.	PMID[16724849]
NPO4331	Plakortis lita	Species	Plakinidae	Eukaryota	n.a.	Okinawan	n.a.	PMID[11277756]
NPO4331	Plakortis lita	Species	Plakinidae	Eukaryota	n.a.	Palauan	n.a.	PMID[10479343]
NPO9215	Papaver glaucum	Species	Papaveraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO772	Bosistoa floydii	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27884	Sphacelaria arctica	Species	Sphacelariaceae	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

Activity Type	# Activity
MIC	1

Activity Type	# Activity
Organism	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	MIC	=	50.0	ug.mL-1	PMID[483101]

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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 NPC113550 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	525
0.1-0.2	1591
0.2-0.3	4444
0.3-0.4	11315
0.4-0.5	7666
0.5-0.6	6527
0.6-0.7	8174
0.7-0.8	1958
0.8-0.85	371
0.85-0.9	101
0.9-0.95	21
0.95-1	4

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Similarity Score	Similarity Level	Natural Product ID
0.9847	High Similarity	NPC121651
0.9771	High Similarity	NPC25333
0.9771	High Similarity	NPC49235
0.9771	High Similarity	NPC148893
0.9695	High Similarity	NPC31530

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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 NPC113550 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	397
0.1-0.2	871
0.2-0.3	2039
0.3-0.4	2913
0.4-0.5	1578
0.5-0.6	956
0.6-0.7	360
0.7-0.8	32
0.8-0.85	4
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8421	Intermediate Similarity	NPD3705	Approved
0.8235	Intermediate Similarity	NPD4966	Approved
0.8235	Intermediate Similarity	NPD4965	Approved
0.8235	Intermediate Similarity	NPD4967	Phase 2
0.8129	Intermediate Similarity	NPD6234	Discontinued

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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