NPASS Compound

Structure

NPC224454 OpenBabel06302215582D 33 36 0 0 1 0 0 0 0 0999 V2000 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.0000 -2.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -0.8660 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -1.7321 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -0.5000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 -6.9282 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.6603 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.9282 1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -9.5263 1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 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 -1.7321 -2.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -2.0000 0.0000 O 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 4 2 0 0 0 0 5 3 1 6 0 0 0 5 6 1 0 0 0 0 5 30 1 0 0 0 0 6 7 1 0 0 0 0 6 33 1 1 0 0 0 7 8 1 0 0 0 0 7 32 1 6 0 0 0 8 9 1 0 0 0 0 8 31 1 1 0 0 0 9 10 1 6 0 0 0 9 30 1 0 0 0 0 10 11 1 0 0 0 0 11 28 2 0 0 0 0 11 12 1 0 0 0 0 12 13 2 0 0 0 0 13 14 1 0 0 0 0 13 29 1 0 0 0 0 14 27 2 0 0 0 0 14 15 1 0 0 0 0 15 16 2 0 0 0 0 15 17 1 0 0 0 0 17 18 1 0 0 0 0 18 19 1 6 0 0 0 18 26 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 21 22 1 0 0 0 0 22 23 2 0 0 0 0 22 25 1 0 0 0 0 23 24 1 0 0 0 0 26 27 1 0 0 0 0 27 28 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	462.12
Volume:	430.443
LogP:	1.254
LogD:	1.199
LogS:	-4.074
# Rotatable Bonds:	5
TPSA:	172.21
# H-Bond Aceptor:	11
# H-Bond Donor:	5
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.392
Synthetic Accessibility Score:	4.106
Fsp3:	0.364
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.407
MDCK Permeability:	2.4351362299057655e-05
Pgp-inhibitor:	0.022
Pgp-substrate:	0.029
Human Intestinal Absorption (HIA):	0.279
20% Bioavailability (F20%):	0.004
30% Bioavailability (F30%):	0.984

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.119
Plasma Protein Binding (PPB):	85.00371551513672%
Volume Distribution (VD):	0.66
Pgp-substrate:	10.302932739257812%

ADMET: Metabolism

CYP1A2-inhibitor:	0.081
CYP1A2-substrate:	0.095
CYP2C19-inhibitor:	0.176
CYP2C19-substrate:	0.08
CYP2C9-inhibitor:	0.299
CYP2C9-substrate:	0.781
CYP2D6-inhibitor:	0.344
CYP2D6-substrate:	0.257
CYP3A4-inhibitor:	0.197
CYP3A4-substrate:	0.124

ADMET: Excretion

Clearance (CL):	6.567
Half-life (T1/2):	0.614

ADMET: Toxicity

hERG Blockers:	0.082
Human Hepatotoxicity (H-HT):	0.603
Drug-inuced Liver Injury (DILI):	0.956
AMES Toxicity:	0.222
Rat Oral Acute Toxicity:	0.129
Maximum Recommended Daily Dose:	0.026
Skin Sensitization:	0.117
Carcinogencity:	0.628
Eye Corrosion:	0.003
Eye Irritation:	0.083
Respiratory Toxicity:	0.119

Download Data

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

Natural Product: NPC224454

Natural Product ID:	NPC224454
*Common Name:**	VXDMNDDYZSDEEQ-CYCKLWOHSA-N
IUPAC Name:	n.a.
Synonyms:
Standard InCHIKey:	VXDMNDDYZSDEEQ-CYCKLWOHSA-N
Standard InCHI:	InChI=1S/C22H22O11/c1-30-21(29)20-18(27)17(26)19(28)22(33-20)31-11-6-12(24)16-13(25)8-14(32-15(16)7-11)9-2-4-10(23)5-3-9/h2-7,14,17-20,22-24,26-28H,8H2,1H3/t14-,17+,18+,19-,20+,22-/m1/s1
SMILES:	COC(=O)[C@@H]1[C@H]([C@@H]([C@H]([C@H](Oc2cc(c3C(=O)C[C@H](c4ccc(cc4)O)Oc3c2)O)O1)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	n.a.
PubChem CID:	53465591
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0001111] Flavonoid glycosides [CHEMONTID:0001583] Flavonoid O-glycosides [CHEMONTID:0002934] Flavonoid O-glucuronides [CHEMONTID:0003534] Flavonoid-7-O-glucuronides

*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
NPO11682	Eusynstyela latericius	Species	Styelidae	Eukaryota	n.a.	n.a.	n.a.	PMID[19505081]
NPO11682	Eusynstyela latericius	Species	Styelidae	Eukaryota	n.a.	Hixson Island (2145.0' S, 15017.5' E); Percy Island Group in the Central Great Barrier Reef, Queensland, Australia; Rib Reef (1828.7' S, 14652.3' E)	n.a.	PMID[19505081]
NPO13664	Garcinia prainiana	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO14421	Vellozia compacta	Species	Velloziaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO4680	Neatostema apulum	Species	Boraginaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO15065	Daniellia ogea	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO9336	Rhodococcus jostii	Species	0cardiaceae	Bacteria	n.a.	n.a.	n.a.	Database[UNPD]
NPO11682	Eusynstyela latericius	Species	Styelidae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO17151	Schizaphis graminum	Species	Aphididae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO13172	Xylaria telfairii	Species	Xylariaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO10893	Polyporus ciliatus	Species	Polyporaceae	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 NPC224454 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	359
0.1-0.2	1526
0.2-0.3	3679
0.3-0.4	8282
0.4-0.5	9767
0.5-0.6	4749
0.6-0.7	5461
0.7-0.8	5890
0.8-0.85	2014
0.85-0.9	763
0.9-0.95	195
0.95-1	12

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 NPC224454 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	309
0.1-0.2	875
0.2-0.3	1779
0.3-0.4	2629
0.4-0.5	1962
0.5-0.6	1054
0.6-0.7	354
0.7-0.8	147
0.8-0.85	26
0.85-0.9	15
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