NPASS Compound

Structure

NPC185201 OpenBabel06302216012D 38 42 0 0 1 0 0 0 0 0999 V2000 0.8459 -1.4651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.9767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8459 -1.4651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6918 -0.9767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3835 -1.9535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3835 -2.9302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5377 -3.4186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5377 -4.3953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6918 -4.8837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8459 -4.3953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8459 -3.4186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.1309 -3.4186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3575 -2.5727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6918 -2.9302 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.3835 -4.8837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.2294 -4.3953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0753 -4.8837 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0753 -5.8605 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9212 -4.3953 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.9212 -3.4186 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -6.7671 -2.9302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6130 -3.4186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.4589 -2.9302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.4589 -1.9535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6130 -1.4651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.7671 -1.9535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.0753 -2.9302 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.2294 -3.4186 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3835 -5.8605 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6918 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8459 0.4884 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8459 1.4651 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 1.9535 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6918 1.9535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8459 0.4884 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5377 0.4884 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8459 -2.4419 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 35 2 0 0 0 0 2 3 1 0 0 0 0 3 4 2 0 0 0 0 3 38 1 0 0 0 0 4 5 1 0 0 0 0 4 30 1 0 0 0 0 5 6 1 0 0 0 0 6 28 2 0 0 0 0 6 7 1 0 0 0 0 7 14 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 15 1 0 0 0 0 9 10 2 0 0 0 0 10 11 1 0 0 0 0 11 12 1 0 0 0 0 11 13 1 0 0 0 0 11 14 1 0 0 0 0 15 16 2 0 0 0 0 15 29 1 0 0 0 0 16 28 1 0 0 0 0 16 17 1 0 0 0 0 17 18 2 0 0 0 0 17 19 1 0 0 0 0 19 20 1 0 0 0 0 20 21 1 1 0 0 0 20 27 1 0 0 0 0 21 26 2 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 23 24 1 0 0 0 0 24 25 2 0 0 0 0 25 26 1 0 0 0 0 27 28 1 0 0 0 0 30 31 2 0 0 0 0 30 37 1 0 0 0 0 31 32 1 0 0 0 0 31 35 1 0 0 0 0 32 33 2 0 0 0 0 32 34 1 0 0 0 0 35 36 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	256.11
Volume:	270.175
LogP:	3.486
LogD:	3.283
LogS:	-3.305
# Rotatable Bonds:	2
TPSA:	49.69
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	3
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.868
Synthetic Accessibility Score:	2.651
Fsp3:	0.25
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.664
MDCK Permeability:	1.534178591100499e-05
Pgp-inhibitor:	0.054
Pgp-substrate:	0.007
Human Intestinal Absorption (HIA):	0.011
20% Bioavailability (F20%):	0.993
30% Bioavailability (F30%):	0.967

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.096
Plasma Protein Binding (PPB):	96.73839569091797%
Volume Distribution (VD):	0.875
Pgp-substrate:	3.402529716491699%

ADMET: Metabolism

CYP1A2-inhibitor:	0.982
CYP1A2-substrate:	0.486
CYP2C19-inhibitor:	0.957
CYP2C19-substrate:	0.109
CYP2C9-inhibitor:	0.717
CYP2C9-substrate:	0.92
CYP2D6-inhibitor:	0.968
CYP2D6-substrate:	0.925
CYP3A4-inhibitor:	0.693
CYP3A4-substrate:	0.387

ADMET: Excretion

Clearance (CL):	17.729
Half-life (T1/2):	0.798

ADMET: Toxicity

hERG Blockers:	0.097
Human Hepatotoxicity (H-HT):	0.052
Drug-inuced Liver Injury (DILI):	0.027
AMES Toxicity:	0.33
Rat Oral Acute Toxicity:	0.072
Maximum Recommended Daily Dose:	0.73
Skin Sensitization:	0.936
Carcinogencity:	0.754
Eye Corrosion:	0.006
Eye Irritation:	0.952
Respiratory Toxicity:	0.101

Download Data

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

Natural Product: NPC185201

Natural Product ID:	NPC185201
*Common Name:**	AKTBFFHJRRKAMX-NRFANRHFSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	AKTBFFHJRRKAMX-NRFANRHFSA-N
Standard InCHI:	InChI=1S/C30H28O8/c1-14-24(33)18(27(36)22(15(2)31)25(14)34)12-19-28-17(10-11-30(3,4)38-28)26(35)23-20(32)13-21(37-29(19)23)16-8-6-5-7-9-16/h5-11,21,33-36H,12-13H2,1-4H3/t21-/m0/s1
SMILES:	Cc1c(c(Cc2c3c(C=CC(C)(C)O3)c(c3C(=O)C[C@@H](c4ccccc4)Oc23)O)c(c(C(=O)C)c1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	n.a.
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0003520] Pyranoflavonoids

*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
NPO28717	Miconia myriantha	Species	Melastomataceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11678651]
NPO29049	Sinoadina racemosa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29365	Baileya multiradiata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29331	Pyrrosia sheareri	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO28899	Eupatorium hyssopifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29049	Sinoadina racemosa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29331	Pyrrosia sheareri	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29365	Baileya multiradiata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO28899	Eupatorium hyssopifolium	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29331	Pyrrosia sheareri	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29365	Baileya multiradiata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29331	Pyrrosia sheareri	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO28884	Cladonia cryptochlorophaea	Species	Cladoniaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29365	Baileya multiradiata	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29345	Maytenus horrida	Species	Celastraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29204	Picea breweriana	Species	Pinaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29467	Virola elongata	Species	Myristicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29259	Streptomyces toyocaensis	Species	Streptomycetaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO29444	Erigeron linifolius	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27663	Onoseris lopezii	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29049	Sinoadina racemosa	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29331	Pyrrosia sheareri	Species	Polypodiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28806	Populus grandidentata	Species	Salicaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28717	Miconia myriantha	Species	Melastomataceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO28899	Eupatorium hyssopifolium	Species	Asteraceae	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

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

☑ 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 NPC185201 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	372
0.1-0.2	1503
0.2-0.3	3663
0.3-0.4	9645
0.4-0.5	9149
0.5-0.6	3760
0.6-0.7	6022
0.7-0.8	5172
0.8-0.85	1971
0.85-0.9	962
0.9-0.95	441
0.95-1	37

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 NPC185201 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	329
0.1-0.2	932
0.2-0.3	1497
0.3-0.4	2635
0.4-0.5	1984
0.5-0.6	1156
0.6-0.7	415
0.7-0.8	159
0.8-0.85	20
0.85-0.9	18
0.9-0.95	4
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