NPASS Compound

Structure

NPC57187 OpenBabel06302216012D 37 40 0 0 1 0 0 0 0 0999 V2000 1.4067 4.3776 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4067 4.3776 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0933 3.5116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.4067 2.6456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0933 1.7796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0933 1.7796 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5933 2.6456 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.0933 3.5116 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5933 4.3776 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.4067 0.9135 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 1.4013 0.8090 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.0704 1.5522 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0485 1.3443 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7177 2.0874 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 3.4087 3.0385 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 4.0778 3.7816 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 5.0559 3.5737 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 5.3649 2.6226 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 6.3431 2.4147 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.0122 3.1579 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.6958 1.8795 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.7251 4.3168 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 3.7688 4.7327 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.4305 3.2464 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6092 -0.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4752 -0.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.4752 -1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3412 -2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.3412 -3.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2072 -3.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.0733 -3.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.6092 -2.1691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7431 -1.6691 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7431 -0.6691 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 -0.1229 -2.1691 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9889 -1.6691 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 5 1 1 0 0 0 10 11 1 0 0 0 0 10 35 1 0 0 0 0 11 12 1 6 0 0 0 11 25 1 0 0 0 0 12 13 1 0 0 0 0 14 13 1 1 0 0 0 14 15 1 0 0 0 0 14 21 1 0 0 0 0 15 16 1 0 0 0 0 15 24 1 6 0 0 0 16 17 1 0 0 0 0 16 23 1 1 0 0 0 17 18 1 0 0 0 0 17 22 1 6 0 0 0 18 19 1 1 0 0 0 18 21 1 0 0 0 0 19 20 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:	0.777
LogD:	0.916
LogS:	-3.099
# 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:	0.272
Synthetic Accessibility Score:	4.446
Fsp3:	0.462
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:	-5.855
MDCK Permeability:	1.1296110642433632e-05
Pgp-inhibitor:	0.005
Pgp-substrate:	0.989
Human Intestinal Absorption (HIA):	0.75
20% Bioavailability (F20%):	0.064
30% Bioavailability (F30%):	0.899

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.403
Plasma Protein Binding (PPB):	69.14461517333984%
Volume Distribution (VD):	0.308
Pgp-substrate:	21.121915817260742%

ADMET: Metabolism

CYP1A2-inhibitor:	0.019
CYP1A2-substrate:	0.246
CYP2C19-inhibitor:	0.013
CYP2C19-substrate:	0.548
CYP2C9-inhibitor:	0.005
CYP2C9-substrate:	0.346
CYP2D6-inhibitor:	0.003
CYP2D6-substrate:	0.195
CYP3A4-inhibitor:	0.057
CYP3A4-substrate:	0.399

ADMET: Excretion

Clearance (CL):	3.833
Half-life (T1/2):	0.783

ADMET: Toxicity

hERG Blockers:	0.3
Human Hepatotoxicity (H-HT):	0.271
Drug-inuced Liver Injury (DILI):	0.535
AMES Toxicity:	0.626
Rat Oral Acute Toxicity:	0.054
Maximum Recommended Daily Dose:	0.115
Skin Sensitization:	0.802
Carcinogencity:	0.707
Eye Corrosion:	0.003
Eye Irritation:	0.022
Respiratory Toxicity:	0.024

Download Data

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

Natural Product: NPC57187

Natural Product ID:	NPC57187
*Common Name:**	HCCQMPYJVVKWJT-AQRJENMISA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	HCCQMPYJVVKWJT-AQRJENMISA-N
Standard InCHI:	InChI=1S/C26H32O11/c1-33-18-10-14(5-6-17(18)29)24-16(12-35-26-23(32)22(31)21(30)20(11-28)36-26)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](CO[C@H]2[C@@H]([C@H]([C@@H]([C@@H](CO)O2)O)O)O)c2cc(/C=C/CO)cc(c2O1)OC
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	13648576
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

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	Whole plant	n.a.	n.a.	PMID[16643038]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[20038159]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	aerial part	n.a.	n.a.	PMID[25442304]
NPO27759	Fusarium poae	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25475336]
NPO27022	Neisseria meningitidis	Species	Neisseriaceae	Bacteria	n.a.	n.a.	n.a.	PMID[4990768]
NPO27523	Brickellia glutinosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[6436442]
NPO27416	Ceratonia siliqua	Species	Fabaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO27416	Ceratonia siliqua	Species	Fabaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO27416	Ceratonia siliqua	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO27416	Ceratonia siliqua	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27416	Ceratonia siliqua	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27416	Ceratonia siliqua	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO27022	Neisseria meningitidis	Species	Neisseriaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
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]
NPO29171	Ascochyta salicorniae	Species	Didymellaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27523	Brickellia glutinosa	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO27759	Fusarium poae	Species	Nectriaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO29221	Sarcandra glabra	Species	Chloranthaceae	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 NPC57187 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	423
0.1-0.2	1485
0.2-0.3	3716
0.3-0.4	9493
0.4-0.5	9049
0.5-0.6	4663
0.6-0.7	7926
0.7-0.8	4630
0.8-0.85	877
0.85-0.9	350
0.9-0.95	66
0.95-1	19

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 NPC57187 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	344
0.1-0.2	819
0.2-0.3	1767
0.3-0.4	2776
0.4-0.5	1751
0.5-0.6	970
0.6-0.7	597
0.7-0.8	119
0.8-0.85	6
0.85-0.9	1
0.9-0.95	0
0.95-1	0

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