NPASS Compound

Structure

NPC91114 OpenBabel06302216222D 34 38 0 0 0 0 0 0 0 0999 V2000 5.0389 -1.8429 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5007 -1.0431 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4242 -1.0431 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0389 -0.2433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1154 -0.2433 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1919 -1.8429 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.3921 -1.3811 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5883 -1.8454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5884 -2.7679 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7895 -1.3842 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7945 -0.4587 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5907 0.0036 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3896 -0.4576 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.5902 0.9195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.3889 1.3810 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.7957 1.3782 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0070 0.9260 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8058 1.3872 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8118 2.3097 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6032 0.9128 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.4041 1.3705 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.6071 -0.0006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8082 -0.4618 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7985 -1.3830 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5949 -1.8485 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.0040 -1.8417 0.0000 O 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 3.6537 0.5565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.7302 0.5565 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 4.1154 1.3562 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.6537 2.1560 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.0389 1.3562 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5007 2.1560 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 5.5007 0.5565 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 4 34 1 0 0 0 0 4 5 2 0 0 0 0 5 6 1 0 0 0 0 5 28 1 0 0 0 0 6 7 1 0 0 0 0 7 13 1 0 0 0 0 7 8 2 0 0 0 0 8 9 1 0 0 0 0 8 10 1 0 0 0 0 10 26 1 0 0 0 0 10 11 2 0 0 0 0 11 27 1 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 12 14 1 0 0 0 0 14 15 2 0 0 0 0 14 16 1 0 0 0 0 16 17 1 0 0 0 0 17 27 1 0 0 0 0 17 18 2 0 0 0 0 18 19 1 0 0 0 0 18 20 1 0 0 0 0 20 21 1 0 0 0 0 20 22 2 0 0 0 0 22 23 1 0 0 0 0 23 24 1 0 0 0 0 23 27 2 0 0 0 0 24 25 2 0 0 0 0 24 26 1 0 0 0 0 28 29 1 0 0 0 0 28 30 2 0 0 0 0 30 31 1 0 0 0 0 30 32 1 0 0 0 0 32 33 1 0 0 0 0 32 34 2 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	470.01
Volume:	411.625
LogP:	1.301
LogD:	0.481
LogS:	-4.828
# Rotatable Bonds:	3
TPSA:	228.33
# H-Bond Aceptor:	13
# H-Bond Donor:	7
# Rings:	5
# Heavy Atoms:	13

MedChem Properties

QED Drug-Likeness Score:	0.114
Synthetic Accessibility Score:	3.274
Fsp3:	0.0
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	2
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.964
MDCK Permeability:	8.29244436317822e-06
Pgp-inhibitor:	0.001
Pgp-substrate:	0.261
Human Intestinal Absorption (HIA):	0.794
20% Bioavailability (F20%):	0.643
30% Bioavailability (F30%):	0.999

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.007
Plasma Protein Binding (PPB):	85.25557708740234%
Volume Distribution (VD):	0.547
Pgp-substrate:	36.8952751159668%

ADMET: Metabolism

CYP1A2-inhibitor:	0.247
CYP1A2-substrate:	0.068
CYP2C19-inhibitor:	0.01
CYP2C19-substrate:	0.031
CYP2C9-inhibitor:	0.507
CYP2C9-substrate:	0.045
CYP2D6-inhibitor:	0.0
CYP2D6-substrate:	0.078
CYP3A4-inhibitor:	0.009
CYP3A4-substrate:	0.003

ADMET: Excretion

Clearance (CL):	1.715
Half-life (T1/2):	0.928

ADMET: Toxicity

hERG Blockers:	0.005
Human Hepatotoxicity (H-HT):	0.91
Drug-inuced Liver Injury (DILI):	0.998
AMES Toxicity:	0.043
Rat Oral Acute Toxicity:	0.055
Maximum Recommended Daily Dose:	0.739
Skin Sensitization:	0.916
Carcinogencity:	0.055
Eye Corrosion:	0.004
Eye Irritation:	0.876
Respiratory Toxicity:	0.025

Download Data

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

Natural Product: NPC91114

Natural Product ID:	NPC91114
*Common Name:**	BPAOAXAAABIQKR-UHFFFAOYSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	BPAOAXAAABIQKR-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C21H10O13/c22-7-2-6(19(28)29)16(15(27)12(7)24)32-9-3-5-11-10-4(20(30)34-18(11)14(9)26)1-8(23)13(25)17(10)33-21(5)31/h1-3,22-27H,(H,28,29)
SMILES:	c1c2c3c4c(cc(c(c4oc2=O)O)Oc2c(cc(c(c2O)O)O)C(=O)O)c(=O)oc3c(c1O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	10151874
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000238] Tannins [CHEMONTID:0001710] Hydrolyzable tannins

*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
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	fruit	n.a.	DOI[10.1007/s00217-007-0799-1]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	flower	n.a.	DOI[10.1016/j.foodchem.2011.01.077]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	PMID[11520216]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[1402962]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	n.a.	bark	n.a.	PMID[14727919]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	n.a.	root	n.a.	PMID[14727919]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	n.a.	leaf	n.a.	PMID[14727919]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	n.a.	xylem	n.a.	PMID[14727919]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Seeds	n.a.	n.a.	PMID[15620261]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	n.a.	pericarp	n.a.	PMID[18496782]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[25466114]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Flower Buds	n.a.	n.a.	PMID[26977531]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	Flowers	n.a.	n.a.	PMID[28737396]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[8904847]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	n.a.	leaf	n.a.	Database[Article]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Stem	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Stem Bark	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Bark	n.a.	n.a.	Database[FooDB]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	Stem Bark	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Bark	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	Testa	n.a.	n.a.	Database[FooDB]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	Embryo	n.a.	n.a.	Database[FooDB]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Twig	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Essential Oil	n.a.	n.a.	Database[FooDB]
NPO41166	Juglans ailanthifolia	Species	Juglandaceae	Eukaryota		n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.		Database[FooDB]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	Fruit	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	Leaf	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Pericarp	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Root Bark	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	Seed	n.a.	n.a.	Database[FooDB]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.		Database[Phenol-Explorer]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	Fruits	n.a.		Database[Phenol-Explorer]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO18674	Juglans regia	Species	Juglandaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[TM-MC]
NPO3987	Syzygium aromaticum	Species	Myrtaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO21349	Punica granatum	Species	Lythraceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO18674	Juglans regia	Species	Juglandaceae	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
NPO3987	NPC91114	Other	Leaf	18	18	18	mg/100g	Database [DUKE]
NPO41166	NPC91114	Other	n.a.	89.74613444	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]
NPO18674	NPC91114	Other	n.a.	196.8708649	n.a.	n.a.	mg/100g	Database [PHENOL EXPLORER]

☑ 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 NPC91114 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	617
0.1-0.2	2496
0.2-0.3	5967
0.3-0.4	11347
0.4-0.5	5499
0.5-0.6	4434
0.6-0.7	5506
0.7-0.8	4696
0.8-0.85	1577
0.85-0.9	511
0.9-0.95	42
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 NPC91114 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	511
0.1-0.2	1155
0.2-0.3	2275
0.3-0.4	2656
0.4-0.5	1509
0.5-0.6	709
0.6-0.7	203
0.7-0.8	105
0.8-0.85	20
0.85-0.9	6
0.9-0.95	0
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