NPASS Compound

Structure

CID22195 OpenBabel06191715352D 31 34 0 0 1 0 0 0 0 0999 V2000 -6.9282 -4.0000 0.0000 C 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 -1.7321 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.1962 -4.0000 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 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 -3.0000 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 1.7321 0.0000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -2.5981 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -1.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 0.8660 -1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0 -3.4641 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -1.0000 0.0000 C 0 0 1 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 -4.3301 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.5981 -4.5000 0.0000 O 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 -3.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -6.0622 -4.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 -1.5000 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 28 1 0 0 0 0 2 3 2 0 0 0 0 2 8 1 0 0 0 0 3 10 1 0 0 0 0 4 7 2 0 0 0 0 4 9 1 0 0 0 0 5 7 1 0 0 0 0 5 11 2 0 0 0 0 6 21 1 0 0 0 0 7 28 1 0 0 0 0 8 19 2 0 0 0 0 8 22 1 0 0 0 0 9 13 2 0 0 0 0 9 23 1 0 0 0 0 10 14 2 0 0 0 0 10 30 1 0 0 0 0 11 13 1 0 0 0 0 11 29 1 0 0 0 0 12 6 1 1 0 0 0 12 15 1 0 0 0 0 12 31 1 0 0 0 0 13 16 1 0 0 0 0 14 16 1 0 0 0 0 14 19 1 0 0 0 0 15 17 1 0 0 0 0 15 24 1 6 0 0 0 16 25 2 0 0 0 0 17 18 1 0 0 0 0 17 26 1 1 0 0 0 18 20 1 0 0 0 0 18 27 1 6 0 0 0 19 29 1 0 0 0 0 20 30 1 1 0 0 0 20 31 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	436.1
Volume:	398.488
LogP:	0.985
LogD:	0.399
LogS:	-3.664
# Rotatable Bonds:	4
TPSA:	179.28
# H-Bond Aceptor:	11
# H-Bond Donor:	6
# Rings:	4
# Heavy Atoms:	11

MedChem Properties

QED Drug-Likeness Score:	0.292
Synthetic Accessibility Score:	3.97
Fsp3:	0.35
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-6.221
MDCK Permeability:	1.32585382743855e-05
Pgp-inhibitor:	0.007
Pgp-substrate:	0.989
Human Intestinal Absorption (HIA):	0.723
20% Bioavailability (F20%):	0.008
30% Bioavailability (F30%):	0.979

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.048
Plasma Protein Binding (PPB):	78.57817077636719%
Volume Distribution (VD):	1.0
Pgp-substrate:	18.678171157836914%

ADMET: Metabolism

CYP1A2-inhibitor:	0.454
CYP1A2-substrate:	0.167
CYP2C19-inhibitor:	0.023
CYP2C19-substrate:	0.075
CYP2C9-inhibitor:	0.051
CYP2C9-substrate:	0.748
CYP2D6-inhibitor:	0.251
CYP2D6-substrate:	0.213
CYP3A4-inhibitor:	0.057
CYP3A4-substrate:	0.019

ADMET: Excretion

Clearance (CL):	4.593
Half-life (T1/2):	0.774

ADMET: Toxicity

hERG Blockers:	0.01
Human Hepatotoxicity (H-HT):	0.178
Drug-inuced Liver Injury (DILI):	0.978
AMES Toxicity:	0.804
Rat Oral Acute Toxicity:	0.037
Maximum Recommended Daily Dose:	0.011
Skin Sensitization:	0.668
Carcinogencity:	0.339
Eye Corrosion:	0.005
Eye Irritation:	0.289
Respiratory Toxicity:	0.045

Download Data

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

Natural Product: NPC22195

Natural Product ID:	NPC22195
*Common Name:**	1,5-Dihydroxy-3-Methoxy-8-[(2R,3S,4R,5R,6S)-3,4,5-Trihydroxy-6-(Hydroxymethyl)Oxan-2-Yl]Oxyxanthen-9-One
IUPAC Name:	1,5-dihydroxy-3-methoxy-8-[(2R,3S,4R,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxyxanthen-9-one
Synonyms:
Standard InCHIKey:	XMVBNLMKPMPWAX-DZUHBENNSA-N
Standard InCHI:	InChI=1S/C20H20O11/c1-28-7-4-9(23)13-11(5-7)29-19-8(22)2-3-10(14(19)16(13)25)30-20-18(27)17(26)15(24)12(6-21)31-20/h2-5,12,15,17-18,20-24,26-27H,6H2,1H3/t12-,15-,17+,18-,20-/m0/s1
SMILES:	COc1cc(c2c(c1)oc1c(ccc(c1c2=O)O[C@@H]1[C@H]([C@@H]([C@H]([C@H](CO)O1)O)O)O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL1901330
PubChem CID:	44144324
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000123] Benzopyrans [CHEMONTID:0003410] 1-benzopyrans [CHEMONTID:0002817] Dibenzopyrans [CHEMONTID:0000200] Xanthenes [CHEMONTID:0000204] Xanthones

*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

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Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO26420	Swertia perennis	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[931752]
NPO28011	Swertia japonica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[5583807]
NPO2743	Swertia purpurascens	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[4527698]
NPO28011	Swertia japonica	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[26996316]
NPO28502	Rhabdastrella globostellata	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[20718449]
NPO28502	Rhabdastrella globostellata	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[20627740]
NPO28502	Rhabdastrella globostellata	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[17524651]
NPO28502	Rhabdastrella globostellata	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[16562838]
NPO28502	Rhabdastrella globostellata	Species	Ancorinidae	Eukaryota	n.a.	n.a.	n.a.	PMID[16499318]
NPO19705	Gentianella campestris	Species	Gentianaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[15490334]

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☑ 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

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Organism ID	NP ID	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference
No data available in table

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☑ 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

Activity Type	# Activity
Potency	3

Activity Type	# Activity
Individual Protein	2
Others	1

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT10	Individual Protein	Geminin	Homo sapiens	Potency	n.a.	517.4	nM	PMID[453245]
NPT755	Individual Protein	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1	Homo sapiens	Potency	n.a.	79432.8	nM	PMID[453245]
NPT2	Others	Unspecified		Potency	n.a.	39810.7	nM	PMID[453245]

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☑ 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 NPC22195 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	444
0.1-0.2	1843
0.2-0.3	4262
0.3-0.4	9981
0.4-0.5	8137
0.5-0.6	4154
0.6-0.7	5249
0.7-0.8	5244
0.8-0.85	1463
0.85-0.9	1236
0.9-0.95	518
0.95-1	166

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC21190
1.0	High Similarity	NPC183357
0.9937	High Similarity	NPC112755
0.9937	High Similarity	NPC471457
0.9937	High Similarity	NPC472381

Showing 1 to 5 of 200 entries

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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 NPC22195 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	406
0.1-0.2	950
0.2-0.3	1988
0.3-0.4	2683
0.4-0.5	1770
0.5-0.6	898
0.6-0.7	294
0.7-0.8	121
0.8-0.85	15
0.85-0.9	15
0.9-0.95	9
0.95-1	1

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.963	High Similarity	NPD7074	Phase 3
0.9568	High Similarity	NPD7054	Approved
0.9509	High Similarity	NPD7472	Approved
0.9455	High Similarity	NPD4338	Clinical (unspecified phase)
0.9387	High Similarity	NPD3818	Discontinued

Showing 1 to 5 of 200 entries

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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