NPASS Compound

Structure

NPC471489 OpenBabel07101718252D 39 42 0 0 1 0 0 0 0 0999 V2000 -0.0000 -4.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 3.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 4.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8660 -2.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 -3.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3660 2.3660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8660 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 7.7942 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 3.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0000 -3.0000 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 2.5981 -1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 6.0622 0.5000 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 3.5000 0.0000 C 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 1.7321 -1.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.4641 2.0000 0.0000 C 0 0 1 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 4.3301 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 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 0.8660 0.5000 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 -0.0000 -1.0000 0.0000 C 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 5.1962 2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8660 -2.5000 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 2.5981 1.5000 0.0000 N 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 -0.8660 -1.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.8660 0.5000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 6.9282 2.0000 0.0000 O 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 1 11 2 0 0 0 0 2 12 2 0 0 0 0 3 18 1 0 0 0 0 4 32 1 0 0 0 0 5 32 1 0 0 0 0 6 33 1 0 0 0 0 7 33 1 0 0 0 0 8 34 1 0 0 0 0 9 38 1 0 0 0 0 10 39 1 0 0 0 0 11 32 1 0 0 0 0 12 33 1 0 0 0 0 13 14 2 0 0 0 0 13 20 1 0 0 0 0 14 21 1 0 0 0 0 15 16 2 0 0 0 0 15 19 1 0 0 0 0 16 23 1 0 0 0 0 17 18 1 0 0 0 0 18 35 2 0 0 0 0 19 20 1 0 0 0 0 19 24 2 0 0 0 0 20 28 2 0 0 0 0 21 25 2 0 0 0 0 21 26 1 0 0 0 0 22 17 1 1 0 0 0 22 24 1 0 0 0 0 22 34 1 0 0 0 0 23 31 2 0 0 0 0 23 38 1 0 0 0 0 24 31 1 0 0 0 0 25 27 1 0 0 0 0 25 28 1 0 0 0 0 26 29 2 0 0 0 0 26 32 1 0 0 0 0 27 30 2 0 0 0 0 27 33 1 0 0 0 0 28 34 1 0 0 0 0 29 30 1 0 0 0 0 29 36 1 0 0 0 0 30 37 1 0 0 0 0 31 39 1 0 0 0 0 M END $$$$

Physi-Chem Properties

Molecular Weight:	529.28
Volume:	571.045
LogP:	6.617
LogD:	3.835
LogS:	-4.917
# Rotatable Bonds:	8
TPSA:	79.23
# H-Bond Aceptor:	6
# H-Bond Donor:	2
# Rings:	4
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.235
Synthetic Accessibility Score:	4.161
Fsp3:	0.364
Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Accepted
GSK Rule:	Rejected
BMS Rule:	0
Golden Triangle Rule:	Rejected
Chelating Alert:	2
PAINS Alert:	1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-4.876
MDCK Permeability:	1.6242194760707207e-05
Pgp-inhibitor:	1.0
Pgp-substrate:	0.009
Human Intestinal Absorption (HIA):	0.582
20% Bioavailability (F20%):	0.563
30% Bioavailability (F30%):	0.614

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.002
Plasma Protein Binding (PPB):	95.70831298828125%
Volume Distribution (VD):	1.034
Pgp-substrate:	8.14692211151123%

ADMET: Metabolism

CYP1A2-inhibitor:	0.377
CYP1A2-substrate:	0.961
CYP2C19-inhibitor:	0.811
CYP2C19-substrate:	0.803
CYP2C9-inhibitor:	0.692
CYP2C9-substrate:	0.95
CYP2D6-inhibitor:	0.791
CYP2D6-substrate:	0.895
CYP3A4-inhibitor:	0.293
CYP3A4-substrate:	0.915

ADMET: Excretion

Clearance (CL):	1.812
Half-life (T1/2):	0.08

ADMET: Toxicity

hERG Blockers:	0.014
Human Hepatotoxicity (H-HT):	0.015
Drug-inuced Liver Injury (DILI):	0.268
AMES Toxicity:	0.03
Rat Oral Acute Toxicity:	0.644
Maximum Recommended Daily Dose:	0.963
Skin Sensitization:	0.365
Carcinogencity:	0.067
Eye Corrosion:	0.003
Eye Irritation:	0.718
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: NPC471489

Natural Product ID:	NPC471489
*Common Name:**	Lucidamine B
IUPAC Name:	1-[(6S)-2,3-dihydroxy-7,8-dimethoxy-5-methyl-1,4-bis(2-methylbut-3-en-2-yl)-6H-benzo[c]phenanthridin-6-yl]propan-2-one
Synonyms:
Standard InCHIKey:	JBKDWQUWYFBOCS-QFIPXVFZSA-N
Standard InCHI:	InChI=1S/C33H39NO5/c1-11-32(4,5)26-21-14-13-20-19-15-16-23(38-9)31(39-10)24(19)22(17-18(3)35)34(8)28(20)25(21)27(30(37)29(26)36)33(6,7)12-2/h11-16,22,36-37H,1-2,17H2,3-10H3/t22-/m0/s1
SMILES:	CC(=O)CC1C2=C(C=CC(=C2OC)OC)C3=C(N1C)C4=C(C=C3)C(=C(C(=C4C(C)(C)C=C)O)O)C(C)(C)C=C
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL252914
PubChem CID:	23656475
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000279] Alkaloids and derivatives [CHEMONTID:0002665] Benzophenanthridine alkaloids [CHEMONTID:0002667] Dihydrobenzophenanthridine alkaloids

*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
NPO2842	Garcinia lucida	Species	Clusiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[17880175]
NPO2842	Garcinia lucida	Species	Clusiaceae	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	3
Others	3

Activity Type	# Activity
Cell Line	1
Organism	5

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Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT189	Cell Line	Vero	Chlorocebus aethiops	IC50	=	17500.0	nM	PMID[482321]
NPT471	Organism	Trypanosoma brucei brucei	Trypanosoma brucei brucei	IC50	=	4100.0	nM	PMID[482321]
NPT633	Organism	Leishmania donovani	Leishmania donovani	IC50	=	6800.0	nM	PMID[482321]
NPT633	Organism	Leishmania donovani	Leishmania donovani	Inhibition	=	64.0	%	PMID[482321]
NPT633	Organism	Leishmania donovani	Leishmania donovani	Inhibition	=	48.0	%	PMID[482321]
NPT633	Organism	Leishmania donovani	Leishmania donovani	Inhibition	=	14.0	%	PMID[482321]

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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 NPC471489 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	338
0.1-0.2	1626
0.2-0.3	6848
0.3-0.4	10726
0.4-0.5	5674
0.5-0.6	13994
0.6-0.7	2944
0.7-0.8	524
0.8-0.85	17
0.85-0.9	2
0.9-0.95	2
0.95-1	2

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Similarity Score	Similarity Level	Natural Product ID
0.9721	High Similarity	NPC17677
0.8978	High Similarity	NPC193906
0.8978	High Similarity	NPC23080
0.8743	High Similarity	NPC33902
0.8743	High Similarity	NPC276674

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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 NPC471489 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	214
0.1-0.2	707
0.2-0.3	923
0.3-0.4	1739
0.4-0.5	2699
0.5-0.6	2196
0.6-0.7	616
0.7-0.8	56
0.8-0.85	0
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
0.7947	Intermediate Similarity	NPD3534	Clinical (unspecified phase)
0.786	Intermediate Similarity	NPD7922	Phase 1
0.7795	Intermediate Similarity	NPD2490	Approved
0.7795	Intermediate Similarity	NPD2488	Approved
0.7619	Intermediate Similarity	NPD2898	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