NPASS Compound

Structure

NPC475085 OpenBabel07101718242D 26 29 0 0 1 0 0 0 0 0999 V2000 -4.0000 -0.7321 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5000 -1.5981 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 -0.5000 1.8660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.5000 0.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.5000 0.1340 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.9504 -2.8271 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.9559 -2.7226 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 -1.0000 1.0000 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 1.7321 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1314 -1.1045 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -3.0000 -0.7321 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 5.5382 -2.0181 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.5491 -1.8090 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 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1369 -1.0000 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 0.8660 -0.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 1.0000 0.0000 C 0 0 3 0 0 0 0 0 0 0 0 0 3.5491 -0.1910 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 6.5327 -2.1226 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 23 1 0 0 0 0 5 6 1 0 0 0 0 5 10 1 0 0 0 0 6 14 2 0 0 0 0 7 8 2 0 0 0 0 7 16 1 0 0 0 0 8 17 1 0 0 0 0 9 11 2 0 0 0 0 9 18 1 0 0 0 0 10 23 1 0 0 0 0 11 23 1 0 0 0 0 12 15 1 0 0 0 0 12 19 2 0 0 0 0 13 16 2 0 0 0 0 13 20 1 0 0 0 0 15 22 2 0 0 0 0 16 25 1 0 0 0 0 17 19 1 0 0 0 0 17 20 2 0 0 0 0 18 21 2 0 0 0 0 18 22 1 0 0 0 0 19 21 1 0 0 0 0 20 24 1 0 0 0 0 21 24 1 0 0 0 0 22 26 1 0 0 0 0 23 26 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	347.19
Volume:	379.624
LogP:	6.516
LogD:	5.001
LogS:	-3.945
# Rotatable Bonds:	3
TPSA:	45.25
# H-Bond Aceptor:	3
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	3

MedChem Properties

QED Drug-Likeness Score:	0.55
Synthetic Accessibility Score:	3.535
Fsp3:	0.304
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.079
MDCK Permeability:	1.583469747856725e-05
Pgp-inhibitor:	0.979
Pgp-substrate:	0.008
Human Intestinal Absorption (HIA):	0.016
20% Bioavailability (F20%):	0.873
30% Bioavailability (F30%):	0.262

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.047
Plasma Protein Binding (PPB):	97.0544662475586%
Volume Distribution (VD):	3.478
Pgp-substrate:	2.437747001647949%

ADMET: Metabolism

CYP1A2-inhibitor:	0.98
CYP1A2-substrate:	0.376
CYP2C19-inhibitor:	0.958
CYP2C19-substrate:	0.249
CYP2C9-inhibitor:	0.811
CYP2C9-substrate:	0.926
CYP2D6-inhibitor:	0.959
CYP2D6-substrate:	0.74
CYP3A4-inhibitor:	0.838
CYP3A4-substrate:	0.21

ADMET: Excretion

Clearance (CL):	10.249
Half-life (T1/2):	0.136

ADMET: Toxicity

hERG Blockers:	0.671
Human Hepatotoxicity (H-HT):	0.954
Drug-inuced Liver Injury (DILI):	0.415
AMES Toxicity:	0.227
Rat Oral Acute Toxicity:	0.635
Maximum Recommended Daily Dose:	0.92
Skin Sensitization:	0.931
Carcinogencity:	0.815
Eye Corrosion:	0.003
Eye Irritation:	0.306
Respiratory Toxicity:	0.968

Download Data

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

Natural Product: NPC475085

Natural Product ID:	NPC475085
*Common Name:**	Sid506292
IUPAC Name:	3,5-dimethyl-3-(4-methylpent-3-enyl)-11H-pyrano[3,2-a]carbazol-9-ol
Synonyms:
Standard InCHIKey:	DWMBXHWBPZZCTN-UHFFFAOYSA-N
Standard InCHI:	InChI=1S/C23H25NO2/c1-14(2)6-5-10-23(4)11-9-18-21-19(12-15(3)22(18)26-23)17-8-7-16(25)13-20(17)24-21/h6-9,11-13,24-25H,5,10H2,1-4H3
SMILES:	CC1=CC2=C(C3=C1OC(C=C3)(C)CCC=C(C)C)NC4=C2C=CC(=C4)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL496633
PubChem CID:	375151
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0000211] Indoles and derivatives [CHEMONTID:0000210] Carbazoles

*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
NPO3118	Murraya euchrestifolia	Species	Rutaceae	Eukaryota	stem bark;fruit	n.a.	n.a.	PMID[10924160]
NPO3118	Murraya euchrestifolia	Species	Rutaceae	Eukaryota	root bark	Kuantaochi, Nantou Hsien, Taiwan	n.a.	PMID[10924160]
NPO3118	Murraya euchrestifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]
NPO3118	Murraya euchrestifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO3118	Murraya euchrestifolia	Species	Rutaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]

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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
AC50	2
EC50	9
GI50	55
IC50	3
Others	1
Potency	35

Activity Type	# Activity
Cell Line	59
Individual Protein	34
Organism	3
Others	9

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT368	Cell Line	SN12C	Homo sapiens	GI50	n.a.	25003.45	nM	PMID[491856]
NPT369	Cell Line	ACHN	Homo sapiens	GI50	n.a.	25003.45	nM	PMID[491856]
NPT371	Cell Line	UO-31	Homo sapiens	GI50	n.a.	25003.45	nM	PMID[491856]
NPT116	Cell Line	HL-60	Homo sapiens	GI50	n.a.	22542.39	nM	PMID[491856]
NPT372	Cell Line	HOP-92	Homo sapiens	GI50	n.a.	25003.45	nM	PMID[491856]
NPT374	Cell Line	SF-539	Homo sapiens	GI50	n.a.	25003.45	nM	PMID[491856]
NPT373	Cell Line	SK-MEL-5	Homo sapiens	GI50	n.a.	25003.45	nM	PMID[491856]
NPT375	Cell Line	Malme-3M	Homo sapiens	GI50	n.a.	25003.45	nM	PMID[491856]
NPT111	Cell Line	K562	Homo sapiens	GI50	n.a.	25003.45	nM	PMID[491856]
NPT377	Cell Line	OVCAR-3	Homo sapiens	GI50	n.a.	25003.45	nM	PMID[491856]

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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 NPC475085 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	549
0.1-0.2	3224
0.2-0.3	13795
0.3-0.4	3822
0.4-0.5	14545
0.5-0.6	4554
0.6-0.7	1715
0.7-0.8	379
0.8-0.85	64
0.85-0.9	20
0.9-0.95	16
0.95-1	14

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Similarity Score	Similarity Level	Natural Product ID
1.0	High Similarity	NPC291535
1.0	High Similarity	NPC475112
0.9667	High Similarity	NPC72211
0.9665	High Similarity	NPC70259
0.962	High Similarity	NPC476106

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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 NPC475085 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	333
0.1-0.2	709
0.2-0.3	865
0.3-0.4	1368
0.4-0.5	2677
0.5-0.6	2208
0.6-0.7	852
0.7-0.8	133
0.8-0.85	5
0.85-0.9	0
0.9-0.95	0
0.95-1	0

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Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.8513	High Similarity	NPD3003	Approved
0.8267	Intermediate Similarity	NPD5903	Approved
0.8267	Intermediate Similarity	NPD5902	Approved
0.8205	Intermediate Similarity	NPD1768	Approved
0.815	Intermediate Similarity	NPD5658	Approved

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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