NPASS Compound

Structure

NPC115624 OpenBabel07101718242D 39 44 0 0 1 0 0 0 0 0999 V2000 0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 3.0000 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 6.9282 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 1.0000 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 -0.8660 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9882 -2.9781 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.2646 2.5827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 -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 5.1962 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.1962 0.0000 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 6.0622 1.5000 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 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 4.3301 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -1.7321 0.0000 0.0000 C 0 0 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 -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 0 0 0 0 0 0 0 0 0 0 3.5870 -2.1691 0.0000 C 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 -1.7321 -2.0000 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 2.6088 -1.9612 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.9937 -3.0827 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 7.6713 1.6691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.2701 2.4781 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 0.8660 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 33 1 0 0 0 0 2 34 1 0 0 0 0 3 11 1 0 0 0 0 4 11 2 0 0 0 0 4 15 1 0 0 0 0 5 12 2 0 0 0 0 5 17 1 0 0 0 0 6 12 1 0 0 0 0 6 18 2 0 0 0 0 7 14 2 0 0 0 0 7 16 1 0 0 0 0 8 28 1 0 0 0 0 9 13 1 0 0 0 0 9 35 1 0 0 0 0 10 36 1 0 0 0 0 10 37 1 0 0 0 0 11 14 1 0 0 0 0 13 3 1 1 0 0 0 13 21 1 0 0 0 0 14 20 1 0 0 0 0 15 16 2 0 0 0 0 15 36 1 0 0 0 0 16 37 1 0 0 0 0 17 25 2 0 0 0 0 17 33 1 0 0 0 0 18 25 1 0 0 0 0 18 34 1 0 0 0 0 19 8 1 6 0 0 0 19 22 1 0 0 0 0 19 38 1 0 0 0 0 20 12 1 6 0 0 0 20 21 1 0 0 0 0 21 26 1 6 0 0 0 22 23 1 0 0 0 0 22 29 1 1 0 0 0 23 24 1 0 0 0 0 23 30 1 6 0 0 0 24 27 1 0 0 0 0 24 31 1 1 0 0 0 25 39 1 0 0 0 0 26 32 2 0 0 0 0 26 35 1 0 0 0 0 27 38 1 0 0 0 0 27 39 1 6 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	546.17
Volume:	511.237
LogP:	0.861
LogD:	1.212
LogS:	-3.441
# Rotatable Bonds:	6
TPSA:	162.6
# H-Bond Aceptor:	12
# H-Bond Donor:	4
# Rings:	6
# Heavy Atoms:	12

MedChem Properties

QED Drug-Likeness Score:	0.362
Synthetic Accessibility Score:	4.492
Fsp3:	0.519
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:	-5.557
MDCK Permeability:	4.685277963289991e-05
Pgp-inhibitor:	0.091
Pgp-substrate:	0.687
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.054

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.065
Plasma Protein Binding (PPB):	92.15547943115234%
Volume Distribution (VD):	0.575
Pgp-substrate:	4.666841506958008%

ADMET: Metabolism

CYP1A2-inhibitor:	0.023
CYP1A2-substrate:	0.921
CYP2C19-inhibitor:	0.022
CYP2C19-substrate:	0.846
CYP2C9-inhibitor:	0.02
CYP2C9-substrate:	0.388
CYP2D6-inhibitor:	0.059
CYP2D6-substrate:	0.204
CYP3A4-inhibitor:	0.753
CYP3A4-substrate:	0.693

ADMET: Excretion

Clearance (CL):	4.467
Half-life (T1/2):	0.21

ADMET: Toxicity

hERG Blockers:	0.249
Human Hepatotoxicity (H-HT):	0.39
Drug-inuced Liver Injury (DILI):	0.278
AMES Toxicity:	0.163
Rat Oral Acute Toxicity:	0.059
Maximum Recommended Daily Dose:	0.917
Skin Sensitization:	0.063
Carcinogencity:	0.237
Eye Corrosion:	0.003
Eye Irritation:	0.011
Respiratory Toxicity:	0.062

Download Data

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

Natural Product: NPC115624

Natural Product ID:	NPC115624
*Common Name:**	4-Demethyl-Deoxypodophyllotoxin-4-O-Beta-D-Glucopyranoside
IUPAC Name:	(5R,5aR,8aR)-5-[3,5-dimethoxy-4-[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyphenyl]-5a,8,8a,9-tetrahydro-5H-[2]benzofuro[5,6-f][1,3]benzodioxol-6-one
Synonyms:
Standard InCHIKey:	QMXNRLBPHJPLKV-QNRBAVQLSA-N
Standard InCHI:	InChI=1S/C27H30O12/c1-33-17-5-12(6-18(34-2)25(17)39-27-24(31)23(30)22(29)19(8-28)38-27)20-14-7-16-15(36-10-37-16)4-11(14)3-13-9-35-26(32)21(13)20/h4-7,13,19-24,27-31H,3,8-10H2,1-2H3/t13-,19+,20+,21-,22+,23-,24+,27-/m0/s1
SMILES:	COc1cc(cc(c1O[C@H]1[C@@H]([C@H]([C@@H]([C@@H](CO)O1)O)O)O)OC)[C@@H]1c2cc3c(cc2C[C@H]2COC(=O)[C@H]12)OCO3
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1778163
PubChem CID:	12311205
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0001392] Lignans, neolignans and related compounds [CHEMONTID:0001511] Lignan 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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO14752	Sinopodophyllum emodi	Species	Berberidaceae	Eukaryota	roots and rhizomes	n.a.	n.a.	PMID[21570846]
NPO14752	Sinopodophyllum emodi	Species	Berberidaceae	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
IC50	2

Activity Type	# Activity
Cell Line	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT165	Cell Line	HeLa	Homo sapiens	IC50	=	870.0	nM	PMID[493440]
NPT91	Cell Line	KB	Homo sapiens	IC50	=	2090.0	nM	PMID[493440]

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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 NPC115624 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	340
0.1-0.2	1343
0.2-0.3	3020
0.3-0.4	6211
0.4-0.5	10375
0.5-0.6	6946
0.6-0.7	7393
0.7-0.8	6319
0.8-0.85	599
0.85-0.9	126
0.9-0.95	19
0.95-1	6

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Similarity Score	Similarity Level	Natural Product ID
0.9806	High Similarity	NPC222531
0.974	High Similarity	NPC100465
0.974	High Similarity	NPC152424
0.9615	High Similarity	NPC116759
0.9615	High Similarity	NPC14294

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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 NPC115624 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	280
0.1-0.2	813
0.2-0.3	1720
0.3-0.4	2609
0.4-0.5	2080
0.5-0.6	1024
0.6-0.7	504
0.7-0.8	107
0.8-0.85	5
0.85-0.9	2
0.9-0.95	6
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9481	High Similarity	NPD4966	Approved
0.9481	High Similarity	NPD4965	Approved
0.9481	High Similarity	NPD4967	Phase 2
0.9434	High Similarity	NPD7228	Approved
0.9359	High 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