NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	463.86
Volume:	313.132
LogP:	5.154
LogD:	3.695
LogS:	-4.786
# Rotatable Bonds:	4
TPSA:	18.46
# H-Bond Aceptor:	2
# H-Bond Donor:	0
# Rings:	2
# Heavy Atoms:	5

MedChem Properties

QED Drug-Likeness Score:	0.404
Synthetic Accessibility Score:	5.657
Fsp3:	0.4
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Rejected
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:	-4.498
MDCK Permeability:	1.2353478268778417e-05
Pgp-inhibitor:	0.998
Pgp-substrate:	0.0
Human Intestinal Absorption (HIA):	0.009
20% Bioavailability (F20%):	0.018
30% Bioavailability (F30%):	0.993

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.656
Plasma Protein Binding (PPB):	98.05767822265625%
Volume Distribution (VD):	2.373
Pgp-substrate:	4.3816680908203125%

ADMET: Metabolism

CYP1A2-inhibitor:	0.749
CYP1A2-substrate:	0.165
CYP2C19-inhibitor:	0.147
CYP2C19-substrate:	0.792
CYP2C9-inhibitor:	0.148
CYP2C9-substrate:	0.011
CYP2D6-inhibitor:	0.007
CYP2D6-substrate:	0.02
CYP3A4-inhibitor:	0.689
CYP3A4-substrate:	0.717

ADMET: Excretion

Clearance (CL):	2.403
Half-life (T1/2):	0.081

ADMET: Toxicity

hERG Blockers:	0.321
Human Hepatotoxicity (H-HT):	0.983
Drug-inuced Liver Injury (DILI):	0.97
AMES Toxicity:	0.227
Rat Oral Acute Toxicity:	0.952
Maximum Recommended Daily Dose:	0.973
Skin Sensitization:	0.964
Carcinogencity:	0.366
Eye Corrosion:	0.541
Eye Irritation:	0.261
Respiratory Toxicity:	0.982

Download Data

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

Natural Product: NPC471460

Natural Product ID:	NPC471460
*Common Name:**	Laurenmariallene
IUPAC Name:	(2S,3aR,6aS)-6-bromo-5-[(1Z,3Z)-4-bromohexa-1,3-dienyl]-2-(3-bromopropa-1,2-dienyl)-2,3,3a,6a-tetrahydrofuro[3,2-b]furan
Synonyms:	Laurenmariallene
Standard InCHIKey:	XESWLEVPFYXKLI-UIRRHHTJSA-N
Standard InCHI:	InChI=1S/C15H15Br3O2/c1-2-10(17)5-3-7-12-14(18)15-13(20-12)9-11(19-15)6-4-8-16/h3,5-8,11,13,15H,2,9H2,1H3/b7-3-,10-5-/t4?,11-,13-,15+/m1/s1
SMILES:	BrC=C=C[C@@H]1C[C@@H]2[C@H](O1)C(=C(O2)/C=CC=C(CC)/Br)Br
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL251224
PubChem CID:	24763477
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000002] Organoheterocyclic compounds [CHEMONTID:0001816] Furofurans

*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
NPO21944	Laurencia mariannensis	Species	Rhodomelaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[18076141]
NPO21944	Laurencia mariannensis	Species	Rhodomelaceae	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

Activity Type	# Activity
Others	1

Activity Type	# Activity
Organism	1

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT19	Organism	Escherichia coli	Escherichia coli	IZ	=	7.0	mm	PMID[509187]

☑ 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 NPC471460 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	193
0.1-0.2	3820
0.2-0.3	20524
0.3-0.4	14580
0.4-0.5	3110
0.5-0.6	452
0.6-0.7	15
0.7-0.8	2
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.697	Remote Similarity	NPC223804
0.6944	Remote Similarity	NPC477431
0.6765	Remote Similarity	NPC474711
0.6765	Remote Similarity	NPC474588
0.6515	Remote Similarity	NPC151923
0.6515	Remote Similarity	NPC9611
0.6479	Remote Similarity	NPC474723
0.6479	Remote Similarity	NPC474729
0.6463	Remote Similarity	NPC8161
0.6447	Remote Similarity	NPC162571
0.6447	Remote Similarity	NPC112983
0.6389	Remote Similarity	NPC90463
0.6389	Remote Similarity	NPC271000
0.6316	Remote Similarity	NPC477423
0.6216	Remote Similarity	NPC276299
0.6184	Remote Similarity	NPC494
0.6164	Remote Similarity	NPC477456
0.6164	Remote Similarity	NPC53136
0.6164	Remote Similarity	NPC173409
0.6164	Remote Similarity	NPC477457
0.6125	Remote Similarity	NPC238554
0.6125	Remote Similarity	NPC225022
0.6081	Remote Similarity	NPC182794
0.6081	Remote Similarity	NPC476589
0.6056	Remote Similarity	NPC133600
0.6053	Remote Similarity	NPC471472
0.6053	Remote Similarity	NPC473294
0.6026	Remote Similarity	NPC159547
0.6	Remote Similarity	NPC52781
0.6	Remote Similarity	NPC37382
0.5974	Remote Similarity	NPC316572
0.5972	Remote Similarity	NPC26223
0.5949	Remote Similarity	NPC146583
0.5946	Remote Similarity	NPC25747
0.5946	Remote Similarity	NPC308457
0.5946	Remote Similarity	NPC148233
0.5909	Remote Similarity	NPC475071
0.5904	Remote Similarity	NPC271632
0.5897	Remote Similarity	NPC325098
0.5897	Remote Similarity	NPC477429
0.5897	Remote Similarity	NPC323677
0.5897	Remote Similarity	NPC473453
0.589	Remote Similarity	NPC15193
0.589	Remote Similarity	NPC217537
0.5875	Remote Similarity	NPC177030
0.5867	Remote Similarity	NPC131174
0.5867	Remote Similarity	NPC220766
0.5857	Remote Similarity	NPC86948
0.5844	Remote Similarity	NPC474823
0.5844	Remote Similarity	NPC280374
0.5844	Remote Similarity	NPC63873
0.5823	Remote Similarity	NPC124072
0.5823	Remote Similarity	NPC269103
0.5811	Remote Similarity	NPC179087
0.5811	Remote Similarity	NPC210303
0.5811	Remote Similarity	NPC473737
0.5811	Remote Similarity	NPC44343
0.5795	Remote Similarity	NPC477428
0.5789	Remote Similarity	NPC191233
0.5789	Remote Similarity	NPC124586
0.5789	Remote Similarity	NPC146811
0.5789	Remote Similarity	NPC469446
0.5775	Remote Similarity	NPC474869
0.5769	Remote Similarity	NPC475004
0.5714	Remote Similarity	NPC474913
0.5696	Remote Similarity	NPC129630
0.5694	Remote Similarity	NPC23418
0.5679	Remote Similarity	NPC474280
0.5679	Remote Similarity	NPC470686
0.5679	Remote Similarity	NPC477422
0.5679	Remote Similarity	NPC107654
0.5663	Remote Similarity	NPC68156
0.5663	Remote Similarity	NPC228902
0.5663	Remote Similarity	NPC24827
0.5658	Remote Similarity	NPC475110
0.5658	Remote Similarity	NPC96414
0.5658	Remote Similarity	NPC19769
0.5658	Remote Similarity	NPC476586
0.5658	Remote Similarity	NPC473722
0.5658	Remote Similarity	NPC470123
0.5641	Remote Similarity	NPC238223
0.5641	Remote Similarity	NPC475760
0.5641	Remote Similarity	NPC470032
0.5625	Remote Similarity	NPC473306
0.5616	Remote Similarity	NPC222852
0.5616	Remote Similarity	NPC159650
0.5616	Remote Similarity	NPC83838
0.5616	Remote Similarity	NPC22897
0.5616	Remote Similarity	NPC478095
0.5616	Remote Similarity	NPC143810
0.5616	Remote Similarity	NPC286189
0.561	Remote Similarity	NPC478193
0.561	Remote Similarity	NPC478195
0.561	Remote Similarity	NPC477421
0.561	Remote Similarity	NPC478194
0.561	Remote Similarity	NPC478191
0.561	Remote Similarity	NPC161038
0.561	Remote Similarity	NPC478196
0.561	Remote Similarity	NPC478192
0.56	Remote Similarity	NPC132243

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 NPC471460 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	175
0.1-0.2	3829
0.2-0.3	4113
0.3-0.4	920
0.4-0.5	112
0.5-0.6	1
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.5915	Remote Similarity	NPD585	Clinical (unspecified phase)

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