NPASS Compound

Structure

CID36217 OpenBabel06191715362D 32 34 0 0 1 0 0 0 0 0999 V2000 -2.5981 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.3301 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 -3.0000 0.0000 C 0 0 0 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 -4.3301 -2.5000 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 2.5981 -1.5000 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 1.7321 -1.0000 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 -2.5981 -1.5000 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 -0.8660 1.5000 0.0000 C 0 0 0 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 -2.5000 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 -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 2.5981 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.7321 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 2.0000 0.0000 C 0 0 0 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 -0.8660 0.5000 0.0000 C 0 0 1 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 -3.4641 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 -0.0000 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 -0.0000 3.0000 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 -4.3301 -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 14 1 0 0 0 0 2 14 1 0 0 0 0 3 15 1 0 0 0 0 4 15 1 0 0 0 0 5 31 1 0 0 0 0 6 8 1 0 0 0 0 6 14 2 0 0 0 0 7 9 1 0 0 0 0 7 15 2 0 0 0 0 8 17 1 0 0 0 0 9 18 1 0 0 0 0 10 11 2 0 0 0 0 10 16 1 0 0 0 0 11 22 1 0 0 0 0 12 19 2 0 0 0 0 12 20 1 0 0 0 0 13 21 1 0 0 0 0 13 23 1 0 0 0 0 16 17 2 0 0 0 0 17 25 1 0 0 0 0 18 19 1 0 0 0 0 18 26 2 0 0 0 0 19 27 1 0 0 0 0 20 24 2 0 0 0 0 20 28 1 0 0 0 0 21 24 1 0 0 0 0 21 29 2 0 0 0 0 22 25 2 0 0 0 0 22 31 1 0 0 0 0 23 16 1 6 0 0 0 23 32 1 0 0 0 0 24 26 1 0 0 0 0 25 30 1 0 0 0 0 26 32 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	438.2
Volume:	461.596
LogP:	6.737
LogD:	3.872
LogS:	-2.957
# Rotatable Bonds:	6
TPSA:	96.22
# H-Bond Aceptor:	6
# H-Bond Donor:	3
# Rings:	3
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.513
Synthetic Accessibility Score:	3.617
Fsp3:	0.346
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	1
Golden Triangle Rule:	Accepted
Chelating Alert:	1
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.814
MDCK Permeability:	1.3804125956085045e-05
Pgp-inhibitor:	0.818
Pgp-substrate:	0.884
Human Intestinal Absorption (HIA):	0.025
20% Bioavailability (F20%):	0.854
30% Bioavailability (F30%):	0.293

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.009
Plasma Protein Binding (PPB):	87.68221282958984%
Volume Distribution (VD):	0.968
Pgp-substrate:	13.5090913772583%

ADMET: Metabolism

CYP1A2-inhibitor:	0.298
CYP1A2-substrate:	0.827
CYP2C19-inhibitor:	0.952
CYP2C19-substrate:	0.144
CYP2C9-inhibitor:	0.909
CYP2C9-substrate:	0.956
CYP2D6-inhibitor:	0.765
CYP2D6-substrate:	0.543
CYP3A4-inhibitor:	0.375
CYP3A4-substrate:	0.203

ADMET: Excretion

Clearance (CL):	16.559
Half-life (T1/2):	0.198

ADMET: Toxicity

hERG Blockers:	0.046
Human Hepatotoxicity (H-HT):	0.906
Drug-inuced Liver Injury (DILI):	0.773
AMES Toxicity:	0.021
Rat Oral Acute Toxicity:	0.816
Maximum Recommended Daily Dose:	0.448
Skin Sensitization:	0.933
Carcinogencity:	0.121
Eye Corrosion:	0.003
Eye Irritation:	0.562
Respiratory Toxicity:	0.943

Download Data

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

Natural Product: NPC36217

Natural Product ID:	NPC36217
*Common Name:**	5,7,3'-Trihydroxy-4'-Methoxy-8,2'-Di(3-Methyl-2-Butenyl)-(2S)-Flavanone
IUPAC Name:	(2S)-5,7-dihydroxy-2-[3-hydroxy-4-methoxy-2-(3-methylbut-2-enyl)phenyl]-8-(3-methylbut-2-enyl)-2,3-dihydrochromen-4-one
Synonyms:
Standard InCHIKey:	LGSFAJAWSUQNON-QHCPKHFHSA-N
Standard InCHI:	InChI=1S/C26H30O6/c1-14(2)6-8-17-16(10-11-22(31-5)25(17)30)23-13-21(29)24-20(28)12-19(27)18(26(24)32-23)9-7-15(3)4/h6-7,10-12,23,27-28,30H,8-9,13H2,1-5H3/t23-/m0/s1
SMILES:	CC(=CCc1c(ccc(c1O)OC)[C@@H]1CC(=O)c2c(cc(c(CC=C(C)C)c2O1)O)O)C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL470666
PubChem CID:	3012486
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0000334] Flavonoids [CHEMONTID:0000337] Flavans [CHEMONTID:0003645] 2'-prenylated flavans [CHEMONTID:0003588] 2'-prenylated flavanones

*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
NPO22556	Dendrolobium lanceolatum	Species	Fabaceae	Eukaryota	n.a.	root	n.a.	PMID[15217275]
NPO32946	dendrolobium tanceolatum	Species	Fabaceae	Eukaryota	roots	n.a.	n.a.	PMID[15217275]
NPO22556	Dendrolobium lanceolatum	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

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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
IC50	2
MIC	1

Activity Type	# Activity
Cell Line	1
Organism	2

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT639	Cell Line	NCI-H187	Homo sapiens	IC50	=	8.1	ug.mL-1	PMID[466427]
NPT485	Organism	Plasmodium falciparum (isolate K1 / Thailand)	Plasmodium falciparum K1	IC50	=	3.3	ug.mL-1	PMID[466427]
NPT88	Organism	Mycobacterium tuberculosis	Mycobacterium tuberculosis	MIC	=	12.5	ug.mL-1	PMID[466427]

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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 NPC36217 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	418
0.1-0.2	1560
0.2-0.3	3787
0.3-0.4	9467
0.4-0.5	8857
0.5-0.6	3137
0.6-0.7	4625
0.7-0.8	5502
0.8-0.85	2926
0.85-0.9	1889
0.9-0.95	453
0.95-1	76

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Similarity Score	Similarity Level	Natural Product ID
0.9869	High Similarity	NPC201800
0.9805	High Similarity	NPC186686
0.9803	High Similarity	NPC210459
0.9801	High Similarity	NPC195796
0.9801	High Similarity	NPC35038

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 NPC36217 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	368
0.1-0.2	935
0.2-0.3	1689
0.3-0.4	2609
0.4-0.5	1802
0.5-0.6	1005
0.6-0.7	520
0.7-0.8	163
0.8-0.85	33
0.85-0.9	20
0.9-0.95	4
0.95-1	2

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.9669	High Similarity	NPD2393	Clinical (unspecified phase)
0.9603	High Similarity	NPD1934	Approved
0.9161	High Similarity	NPD2801	Approved
0.9125	High Similarity	NPD6166	Phase 2
0.9125	High Similarity	NPD6167	Clinical (unspecified phase)

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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