NPASS Compound

Structure

NPC113855 OpenBabel06302215132D 66 74 0 0 1 0 0 0 0 0999 V2000 2.7556 -0.5303 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8371 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8371 1.0606 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7556 1.5909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6741 1.0606 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6741 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.5927 -0.5303 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.5927 1.5909 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.7556 2.6516 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9185 -0.5303 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.9185 -1.5909 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 0.0000 -2.1213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9185 -1.5909 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8371 -2.1213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1494 -1.9469 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9565 -1.2642 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.4513 -0.7558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8667 -1.1586 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.3728 -1.1475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5473 -0.6723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0461 -0.5859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.3703 -0.9746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.1958 -1.4498 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.6970 -1.5362 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5953 -2.0321 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1441 -2.2617 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.9687 -2.8130 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5405 -2.9018 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.7495 -3.4413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.3868 -3.8920 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.8150 -3.8033 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6060 -3.2638 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1050 -3.5531 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.5332 -3.6418 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0319 -3.5180 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5142 -3.1985 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2181 -2.7879 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.2875 -2.7634 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.6219 -3.1434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.6433 -2.8577 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.7009 -1.7866 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8485 -2.7262 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8121 -3.1695 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.9896 -2.1651 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.1501 -4.6296 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.7699 -4.8810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -3.7976 -3.6040 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.1085 -1.6842 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -4.1657 -1.1668 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.9041 -1.9282 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.6138 -2.9484 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.9327 -1.6695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.2229 -0.6494 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.2515 -0.3907 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.9898 -1.1521 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.6996 -2.1723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.6710 -2.4310 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.4379 -2.9337 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -9.0184 -0.8934 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -7.5418 0.6294 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.4154 -0.7935 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.8679 0.1422 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.9185 -0.5303 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 0.0716 -1.0036 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.8083 -2.5474 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1 6 2 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 3 4 1 0 0 0 0 4 5 2 0 0 0 0 4 9 1 0 0 0 0 5 6 1 0 0 0 0 5 8 1 0 0 0 0 6 7 1 0 0 0 0 10 2 1 6 0 0 0 10 11 1 0 0 0 0 10 64 1 0 0 0 0 11 12 1 6 0 0 0 11 44 1 0 0 0 0 12 13 1 0 0 0 0 13 63 2 0 0 0 0 13 14 1 0 0 0 0 14 15 2 0 0 0 0 14 66 1 0 0 0 0 15 16 1 0 0 0 0 16 17 2 0 0 0 0 16 65 1 0 0 0 0 17 63 1 0 0 0 0 18 17 1 6 0 0 0 18 19 1 0 0 0 0 18 48 1 0 0 0 0 19 24 2 0 0 0 0 19 20 1 0 0 0 0 20 21 2 0 0 0 0 20 62 1 0 0 0 0 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 61 1 0 0 0 0 23 24 1 0 0 0 0 24 25 1 0 0 0 0 26 25 1 1 0 0 0 26 27 1 0 0 0 0 26 48 1 0 0 0 0 27 32 2 0 0 0 0 27 28 1 0 0 0 0 28 29 2 0 0 0 0 29 30 1 0 0 0 0 29 47 1 0 0 0 0 30 31 2 0 0 0 0 30 46 1 0 0 0 0 31 32 1 0 0 0 0 31 45 1 0 0 0 0 32 33 1 0 0 0 0 33 34 1 0 0 0 0 34 39 2 0 0 0 0 34 35 1 0 0 0 0 35 36 2 0 0 0 0 36 37 1 0 0 0 0 36 42 1 0 0 0 0 37 38 2 0 0 0 0 38 39 1 0 0 0 0 38 41 1 0 0 0 0 39 40 1 0 0 0 0 42 43 2 0 0 0 0 42 44 1 0 0 0 0 48 49 1 6 0 0 0 49 50 1 0 0 0 0 50 51 2 0 0 0 0 50 52 1 0 0 0 0 52 57 2 0 0 0 0 52 53 1 0 0 0 0 53 54 2 0 0 0 0 54 55 1 0 0 0 0 54 60 1 0 0 0 0 55 56 2 0 0 0 0 55 59 1 0 0 0 0 56 57 1 0 0 0 0 56 58 1 0 0 0 0 63 64 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	298.21
Volume:	323.92
LogP:	3.944
LogD:	3.667
LogS:	-4.614
# Rotatable Bonds:	9
TPSA:	55.76
# H-Bond Aceptor:	4
# H-Bond Donor:	1
# Rings:	1
# Heavy Atoms:	4

MedChem Properties

QED Drug-Likeness Score:	0.549
Synthetic Accessibility Score:	4.36
Fsp3:	0.824
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:	-4.426
MDCK Permeability:	8.070525655057281e-05
Pgp-inhibitor:	0.356
Pgp-substrate:	0.002
Human Intestinal Absorption (HIA):	0.006
20% Bioavailability (F20%):	0.367
30% Bioavailability (F30%):	0.967

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.637
Plasma Protein Binding (PPB):	94.38884735107422%
Volume Distribution (VD):	1.032
Pgp-substrate:	6.242785930633545%

ADMET: Metabolism

CYP1A2-inhibitor:	0.091
CYP1A2-substrate:	0.691
CYP2C19-inhibitor:	0.45
CYP2C19-substrate:	0.819
CYP2C9-inhibitor:	0.4
CYP2C9-substrate:	0.052
CYP2D6-inhibitor:	0.062
CYP2D6-substrate:	0.076
CYP3A4-inhibitor:	0.91
CYP3A4-substrate:	0.389

ADMET: Excretion

Clearance (CL):	11.761
Half-life (T1/2):	0.46

ADMET: Toxicity

hERG Blockers:	0.032
Human Hepatotoxicity (H-HT):	0.15
Drug-inuced Liver Injury (DILI):	0.036
AMES Toxicity:	0.006
Rat Oral Acute Toxicity:	0.044
Maximum Recommended Daily Dose:	0.854
Skin Sensitization:	0.643
Carcinogencity:	0.257
Eye Corrosion:	0.032
Eye Irritation:	0.254
Respiratory Toxicity:	0.891

Download Data

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

Natural Product: NPC113855

Natural Product ID:	NPC113855
*Common Name:**	OLBCNYLXXLYHAI-UOVMKRMJSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	OLBCNYLXXLYHAI-UOVMKRMJSA-N
Standard InCHI:	InChI=1S/C44H32O22/c45-15-7-19(47)30-27(8-15)62-41-17-9-26(54)36(58)37(59)40(17)63-28-6-14(5-25(53)35(28)57)43(60)64-29-10-16-18(46)11-20(48)31(39(16)65-38(29)12-1-21(49)33(55)22(50)2-12)32(30)42(41)66-44(61)13-3-23(51)34(56)24(52)4-13/h1-9,11,29,32,38,41-42,45-59H,10H2/t29-,32-,38-,41-,42-/m1/s1
SMILES:	c1c(cc(c(c1O)O)O)[C@@H]1[C@H]2Cc3c(cc(c([C@H]4c5c(cc(cc5O[C@H](c5cc(c(c(c5Oc5cc(cc(c5O)O)C(=O)O2)O)O)O)[C@@H]4OC(=O)c2cc(c(c(c2)O)O)O)O)O)c3O1)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:0001586] Biflavonoids and polyflavonoids

*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
NPO138	Daphniphyllum paxianum	Species	Daphniphyllaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17887722]
NPO10149	Lespedeza bicolor	Species	Fabaceae	Eukaryota	roots	n.a.	n.a.	PMID[21911291]
NPO1346	Nerine bowdenii	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[22312717]
NPO11877	Penicillium herquei	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26848504]
NPO8752	Xylaria cubensis	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[28802670]
NPO10149	Lespedeza bicolor	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[31675225]
NPO1831	Pseudodistoma arborescens	Species	Pseudodistomidae	Eukaryota	n.a.	n.a.	n.a.	PMID[8450325]
NPO11877	Penicillium herquei	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8609085]
NPO4969	Sesbania bispinosa	Species	Fabaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO8127	Veronica arvensis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO11771	Strophanthus kombe	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO10149	Lespedeza bicolor	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO9153	Sorbaria sorbifolia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO6622	Artemisia klotzchiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO9153	Sorbaria sorbifolia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO8127	Veronica arvensis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO10149	Lespedeza bicolor	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11771	Strophanthus kombe	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO11771	Strophanthus kombe	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO10149	Lespedeza bicolor	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO9153	Sorbaria sorbifolia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO138	Daphniphyllum paxianum	Species	Daphniphyllaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13472	Cotula cinerea	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4969	Sesbania bispinosa	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11877	Penicillium herquei	Species	Aspergillaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8127	Veronica arvensis	Species	Plantaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6622	Artemisia klotzchiana	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO5735	Solidago serotina	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10149	Lespedeza bicolor	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14564	Oophaga pumilio	Species	Dendrobatidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1831	Pseudodistoma arborescens	Species	Pseudodistomidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO6845	Mimusops caffra	Species	Sapotaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO8752	Xylaria cubensis	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11823	Marine actinobacterium	n.a.	n.a.	n.a.	n.a.	n.a.	n.a.	Database[UNPD]
NPO1697	Bitis gabonica	Species	Viperidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21255	Hymenoxys insignis	Species	Asteraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11657	Angelica lucida	Species	Apiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO1346	Nerine bowdenii	Species	Amaryllidaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3995	Limonium sinense	Species	Plumbaginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11771	Strophanthus kombe	Species	Apocynaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9153	Sorbaria sorbifolia	Species	Rosaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO11934	Castanea vesca	Species	Fagaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9252	Adina sessilifolia	Species	Rubiaceae	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 NPC113855 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	433
0.1-0.2	1860
0.2-0.3	4303
0.3-0.4	9882
0.4-0.5	8409
0.5-0.6	3825
0.6-0.7	5538
0.7-0.8	6704
0.8-0.85	1520
0.85-0.9	208
0.9-0.95	10
0.95-1	5

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 NPC113855 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	386
0.1-0.2	995
0.2-0.3	2003
0.3-0.4	2621
0.4-0.5	1764
0.5-0.6	878
0.6-0.7	375
0.7-0.8	106
0.8-0.85	20
0.85-0.9	2
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