NPASS Compound

Structure

CID275680 OpenBabel06191716082D 45 51 0 0 1 0 0 0 0 0999 V2000 -2.4185 4.2224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.2816 1.3885 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4737 1.6188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4185 -1.7776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6169 -1.8881 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6587 2.6652 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3846 3.1290 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.6149 3.2951 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1987 2.8875 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2846 1.7224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.2703 -0.5362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.2846 2.7224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7754 -0.0208 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9574 2.9201 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1412 3.9079 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1507 3.3218 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1676 1.5171 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4185 0.2224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3422 -0.8477 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6865 1.2224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.1936 2.2383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5595 3.7356 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4185 1.2224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5714 -0.3564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5525 1.7224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.4908 3.4706 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8569 3.8154 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5525 2.7224 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 1.8828 0.8541 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 2.0951 3.6535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7513 3.1930 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5525 -0.2776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6865 0.2224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8021 -0.8949 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3777 0.3387 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4913 -0.4507 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7205 0.0406 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4185 3.2224 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.5816 0.6743 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 2.2495 4.6416 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5049 -0.5377 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.5669 2.6144 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.5525 -1.2776 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.3793 -1.8011 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 38 1 0 0 0 0 2 39 1 0 0 0 0 3 42 1 0 0 0 0 4 43 1 0 0 0 0 5 44 1 0 0 0 0 6 8 2 0 0 0 0 6 21 1 0 0 0 0 7 9 2 0 0 0 0 7 22 1 0 0 0 0 8 30 1 0 0 0 0 9 31 1 0 0 0 0 10 12 1 0 0 0 0 10 23 1 0 0 0 0 11 13 1 0 0 0 0 11 24 1 0 0 0 0 12 38 1 0 0 0 0 13 39 1 0 0 0 0 14 21 2 0 0 0 0 14 26 1 0 0 0 0 15 22 2 0 0 0 0 15 27 1 0 0 0 0 16 22 1 0 0 0 0 17 21 1 0 0 0 0 18 23 2 0 0 0 0 18 32 1 0 0 0 0 19 24 2 0 0 0 0 19 34 1 0 0 0 0 20 25 2 0 0 0 0 20 33 1 0 0 0 0 23 25 1 0 0 0 0 24 35 1 0 0 0 0 25 28 1 0 0 0 0 26 27 1 0 0 0 0 26 30 2 0 0 0 0 27 31 2 0 0 0 0 28 16 1 6 0 0 0 28 38 1 0 0 0 0 29 17 1 6 0 0 0 29 35 1 0 0 0 0 29 39 1 0 0 0 0 30 40 1 0 0 0 0 31 42 1 0 0 0 0 32 33 2 0 0 0 0 32 43 1 0 0 0 0 33 45 1 0 0 0 0 34 36 2 0 0 0 0 34 44 1 0 0 0 0 35 37 2 0 0 0 0 36 37 1 0 0 0 0 36 41 1 0 0 0 0 37 45 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	608.29
Volume:	631.71
LogP:	5.932
LogD:	3.906
LogS:	-3.84
# Rotatable Bonds:	3
TPSA:	83.86
# H-Bond Aceptor:	8
# H-Bond Donor:	2
# Rings:	7
# Heavy Atoms:	8

MedChem Properties

QED Drug-Likeness Score:	0.275
Synthetic Accessibility Score:	5.664
Fsp3:	0.351
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.619
MDCK Permeability:	2.036158912233077e-05
Pgp-inhibitor:	0.995
Pgp-substrate:	0.452
Human Intestinal Absorption (HIA):	0.004
20% Bioavailability (F20%):	0.843
30% Bioavailability (F30%):	0.975

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.144
Plasma Protein Binding (PPB):	83.9190444946289%
Volume Distribution (VD):	1.301
Pgp-substrate:	15.482457160949707%

ADMET: Metabolism

CYP1A2-inhibitor:	0.078
CYP1A2-substrate:	0.97
CYP2C19-inhibitor:	0.064
CYP2C19-substrate:	0.949
CYP2C9-inhibitor:	0.043
CYP2C9-substrate:	0.52
CYP2D6-inhibitor:	0.019
CYP2D6-substrate:	0.959
CYP3A4-inhibitor:	0.077
CYP3A4-substrate:	0.949

ADMET: Excretion

Clearance (CL):	10.016
Half-life (T1/2):	0.398

ADMET: Toxicity

hERG Blockers:	0.946
Human Hepatotoxicity (H-HT):	0.083
Drug-inuced Liver Injury (DILI):	0.543
AMES Toxicity:	0.116
Rat Oral Acute Toxicity:	0.305
Maximum Recommended Daily Dose:	0.991
Skin Sensitization:	0.866
Carcinogencity:	0.032
Eye Corrosion:	0.003
Eye Irritation:	0.004
Respiratory Toxicity:	0.386

Download Data

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

Natural Product: NPC275680

Natural Product ID:	NPC275680
*Common Name:**	Tiliageine
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	YZGZHFUKHPDLOJ-WDYNHAJCSA-N
Standard InCHI:	InChI=1S/C37H40N2O6/c1-38-12-10-23-18-32(43-4)33-20-25(23)28(38)16-22-7-9-31(42-3)27(15-22)26-14-21(6-8-30(26)40)17-29-35-24(11-13-39(29)2)19-34(44-5)36(41)37(35)45-33/h6-9,14-15,18-20,28-29,40-41H,10-13,16-17H2,1-5H3/t28-,29+/m1/s1
SMILES:	COc1cc2CCN([C@H]3c2cc1Oc1c2c(CCN([C@H]2Cc2ccc(c(c4cc(C3)ccc4OC)c2)O)C)cc(c1O)OC)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL2262394
PubChem CID:	76315750
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0004603] Organic oxygen compounds [CHEMONTID:0000323] Organooxygen compounds [CHEMONTID:0000254] Ethers [CHEMONTID:0002463] Diarylethers

*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
NPO3595	Euscaphis japonica	Species	Staphyleaceae	Eukaryota	n.a.	pericarp	n.a.	PMID[4421158]
NPO25727	Tabernaemontana divaricata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[30169038]
NPO25727	Tabernaemontana divaricata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26231157]
NPO25727	Tabernaemontana divaricata	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[23944995]
NPO3595	Euscaphis japonica	Species	Staphyleaceae	Eukaryota	Twigs	Yangming mountain, Taiwan	2008-APR	PMID[20873721]
NPO3595	Euscaphis japonica	Species	Staphyleaceae	Eukaryota	n.a.	twig	n.a.	DOI[10.1021/np1003593]
NPO7569	Guatteria boliviana	Species	Annonaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5150	Mephitis mephitis	Species	Mephitidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3436	Taraxacum linearisquameum	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6090	Caulerpa prolifera	Species	Caulerpaceae	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	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
NPT992	Organism	Entamoeba histolytica	Entamoeba histolytica	IC50	=	19.21	ug.mL-1	PMID[483019]

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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 NPC275680 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	365
0.1-0.2	1667
0.2-0.3	8007
0.3-0.4	10341
0.4-0.5	5118
0.5-0.6	7924
0.6-0.7	7369
0.7-0.8	1545
0.8-0.85	172
0.85-0.9	90
0.9-0.95	49
0.95-1	50

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC22115
0.9881	High Similarity	NPC302245
0.9881	High Similarity	NPC95426
0.9881	High Similarity	NPC16357
0.9822	High Similarity	NPC139783

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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 NPC275680 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	212
0.1-0.2	778
0.2-0.3	1151
0.3-0.4	2234
0.4-0.5	2362
0.5-0.6	1542
0.6-0.7	698
0.7-0.8	159
0.8-0.85	7
0.85-0.9	2
0.9-0.95	3
0.95-1	2

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9762	High Similarity	NPD8053	Approved
0.9762	High Similarity	NPD8054	Approved
0.9345	High Similarity	NPD8252	Approved
0.9345	High Similarity	NPD8099	Discontinued
0.9345	High Similarity	NPD8251	Approved

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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