NPASS Compound

Structure

Physi-Chem Properties

Molecular Weight:	248.13
Volume:	240.361
LogP:	-0.274
LogD:	-0.707
LogS:	-0.134
# Rotatable Bonds:	5
TPSA:	99.38
# H-Bond Aceptor:	6
# H-Bond Donor:	4
# Rings:	1
# Heavy Atoms:	6

MedChem Properties

QED Drug-Likeness Score:	0.455
Synthetic Accessibility Score:	3.797
Fsp3:	0.818
Lipinski Rule-of-5:	Accepted
Pfizer Rule:	Accepted
GSK Rule:	Accepted
BMS Rule:	0
Golden Triangle Rule:	Accepted
Chelating Alert:	0
PAINS Alert:	0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:	-5.211
MDCK Permeability:	0.000316074350848794
Pgp-inhibitor:	0.001
Pgp-substrate:	0.003
Human Intestinal Absorption (HIA):	0.568
20% Bioavailability (F20%):	0.676
30% Bioavailability (F30%):	0.705

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.256
Plasma Protein Binding (PPB):	25.273998260498047%
Volume Distribution (VD):	0.493
Pgp-substrate:	75.31130981445312%

ADMET: Metabolism

CYP1A2-inhibitor:	0.018
CYP1A2-substrate:	0.075
CYP2C19-inhibitor:	0.015
CYP2C19-substrate:	0.442
CYP2C9-inhibitor:	0.002
CYP2C9-substrate:	0.098
CYP2D6-inhibitor:	0.005
CYP2D6-substrate:	0.13
CYP3A4-inhibitor:	0.006
CYP3A4-substrate:	0.048

ADMET: Excretion

Clearance (CL):	2.016
Half-life (T1/2):	0.852

ADMET: Toxicity

hERG Blockers:	0.048
Human Hepatotoxicity (H-HT):	0.054
Drug-inuced Liver Injury (DILI):	0.028
AMES Toxicity:	0.393
Rat Oral Acute Toxicity:	0.025
Maximum Recommended Daily Dose:	0.004
Skin Sensitization:	0.152
Carcinogencity:	0.325
Eye Corrosion:	0.025
Eye Irritation:	0.817
Respiratory Toxicity:	0.024

Download Data

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

Natural Product: NPC155457

Natural Product ID:	NPC155457
*Common Name:**	3-Methylbut-3-Enyl-Beta-D-Glucopyranose
IUPAC Name:	(2R,3S,4S,5R,6R)-2-(hydroxymethyl)-6-(3-methylbut-3-enoxy)oxane-3,4,5-triol
Synonyms:
Standard InCHIKey:	XJEVPMIXWZHRML-KAMPLNKDSA-N
Standard InCHI:	InChI=1S/C11H20O6/c1-6(2)3-4-16-11-10(15)9(14)8(13)7(5-12)17-11/h7-15H,1,3-5H2,2H3/t7-,8-,9+,10-,11-/m1/s1
SMILES:	OC[C@H]1O[C@@H](OCCC(=C)C)[C@@H]([C@H]([C@@H]1O)O)O
Synthetic Gene Cluster:	n.a.
ChEMBL Identifier:	CHEMBL388607
PubChem CID:	14239302
Chemical Classification:**	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000012] Lipids and lipid-like molecules [CHEMONTID:0003909] Fatty Acyls [CHEMONTID:0001766] Fatty acyl glycosides [CHEMONTID:0003861] Fatty acyl glycosides of mono- and disaccharides

*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
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	n.a.	leaf	n.a.	PMID[11348221]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	fruit	n.a.	n.a.	PMID[15844957]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	fruits	n.a.	n.a.	PMID[16378361]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	fruits	Tahiti	n.a.	PMID[17378609]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[17480098]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	roots	n.a.	n.a.	PMID[18076142]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[24224843]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[27196335]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	Fruits	n.a.	n.a.	PMID[32083868]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO4323	Morinda citrifolia	Species	Rubiaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCM_Taiwan]
NPO4323	Morinda citrifolia	Species	Rubiaceae	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	6

Activity Type	# Activity
Cell Line	1
Organism	5

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference
NPT80	Cell Line	Raji	Homo sapiens	Activity	=	60.0	%	PMID[545521]
NPT164	Organism	Human herpesvirus 4	Human herpesvirus 4	Activity	=	10.5	%	PMID[545521]
NPT164	Organism	Human herpesvirus 4	Human herpesvirus 4	Activity	=	55.5	%	PMID[545521]
NPT164	Organism	Human herpesvirus 4	Human herpesvirus 4	Activity	=	80.1	%	PMID[545521]
NPT164	Organism	Human herpesvirus 4	Human herpesvirus 4	Activity	=	100.0	%	PMID[545521]
NPT32	Organism	Mus musculus	Mus musculus	ID50	>	1.0	mg	PMID[545521]

☑ 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 NPC155457 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	227
0.1-0.2	4153
0.2-0.3	14359
0.3-0.4	13746
0.4-0.5	7934
0.5-0.6	1912
0.6-0.7	277
0.7-0.8	72
0.8-0.85	12
0.85-0.9	3
0.9-0.95	1
0.95-1	1

Similarity Score	Similarity Level	Natural Product ID
0.9333	High Similarity	NPC147292
0.8852	High Similarity	NPC13143
0.8852	High Similarity	NPC294813
0.8548	High Similarity	NPC31496
0.8393	Intermediate Similarity	NPC124963
0.8393	Intermediate Similarity	NPC233726
0.8393	Intermediate Similarity	NPC23134
0.8095	Intermediate Similarity	NPC277570
0.807	Intermediate Similarity	NPC326533
0.8036	Intermediate Similarity	NPC282143
0.8036	Intermediate Similarity	NPC42503
0.8036	Intermediate Similarity	NPC299781
0.8036	Intermediate Similarity	NPC157193
0.7966	Intermediate Similarity	NPC303727
0.7869	Intermediate Similarity	NPC219040
0.7857	Intermediate Similarity	NPC14144
0.7797	Intermediate Similarity	NPC269166
0.7797	Intermediate Similarity	NPC107914
0.7797	Intermediate Similarity	NPC323361
0.7797	Intermediate Similarity	NPC246558
0.7797	Intermediate Similarity	NPC157514
0.7797	Intermediate Similarity	NPC145112
0.7797	Intermediate Similarity	NPC58629
0.7797	Intermediate Similarity	NPC89145
0.7797	Intermediate Similarity	NPC242073
0.7797	Intermediate Similarity	NPC67660
0.7797	Intermediate Similarity	NPC165198
0.7797	Intermediate Similarity	NPC130683
0.7794	Intermediate Similarity	NPC474078
0.7746	Intermediate Similarity	NPC229655
0.7714	Intermediate Similarity	NPC472174
0.7705	Intermediate Similarity	NPC148424
0.7679	Intermediate Similarity	NPC277475
0.7679	Intermediate Similarity	NPC321087
0.7619	Intermediate Similarity	NPC143326
0.7586	Intermediate Similarity	NPC323574
0.7581	Intermediate Similarity	NPC472025
0.7571	Intermediate Similarity	NPC132938
0.75	Intermediate Similarity	NPC285364
0.75	Intermediate Similarity	NPC289758
0.75	Intermediate Similarity	NPC472026
0.75	Intermediate Similarity	NPC255377
0.75	Intermediate Similarity	NPC92246
0.75	Intermediate Similarity	NPC69445
0.75	Intermediate Similarity	NPC165846
0.75	Intermediate Similarity	NPC21209
0.75	Intermediate Similarity	NPC73906
0.75	Intermediate Similarity	NPC176017
0.75	Intermediate Similarity	NPC199857
0.7467	Intermediate Similarity	NPC280367
0.7465	Intermediate Similarity	NPC472173
0.746	Intermediate Similarity	NPC320032
0.746	Intermediate Similarity	NPC322855
0.7414	Intermediate Similarity	NPC82512
0.7333	Intermediate Similarity	NPC100697
0.7333	Intermediate Similarity	NPC127295
0.7333	Intermediate Similarity	NPC163362
0.7324	Intermediate Similarity	NPC55652
0.7297	Intermediate Similarity	NPC133377
0.726	Intermediate Similarity	NPC326661
0.7231	Intermediate Similarity	NPC477750
0.7231	Intermediate Similarity	NPC477757
0.7231	Intermediate Similarity	NPC477753
0.7231	Intermediate Similarity	NPC477763
0.7231	Intermediate Similarity	NPC477755
0.7231	Intermediate Similarity	NPC477762
0.7188	Intermediate Similarity	NPC317023
0.7188	Intermediate Similarity	NPC290179
0.7188	Intermediate Similarity	NPC34877
0.7162	Intermediate Similarity	NPC110813
0.7143	Intermediate Similarity	NPC320240
0.7143	Intermediate Similarity	NPC20072
0.7143	Intermediate Similarity	NPC70756
0.7089	Intermediate Similarity	NPC470124
0.7089	Intermediate Similarity	NPC470658
0.7089	Intermediate Similarity	NPC73166
0.7069	Intermediate Similarity	NPC230789
0.7069	Intermediate Similarity	NPC252918
0.7015	Intermediate Similarity	NPC325773
0.7013	Intermediate Similarity	NPC16090
0.6964	Remote Similarity	NPC298699
0.6964	Remote Similarity	NPC86191
0.6964	Remote Similarity	NPC134252
0.6964	Remote Similarity	NPC213159
0.6964	Remote Similarity	NPC291502
0.6964	Remote Similarity	NPC317182
0.6962	Remote Similarity	NPC259296
0.6962	Remote Similarity	NPC136699
0.6962	Remote Similarity	NPC98276
0.6962	Remote Similarity	NPC266718
0.6962	Remote Similarity	NPC475035
0.6962	Remote Similarity	NPC220167
0.6957	Remote Similarity	NPC477756
0.6957	Remote Similarity	NPC477751
0.6957	Remote Similarity	NPC477752
0.6957	Remote Similarity	NPC477764
0.6923	Remote Similarity	NPC251026
0.6875	Remote Similarity	NPC477747
0.6875	Remote Similarity	NPC477746
0.6857	Remote Similarity	NPC477759
0.6857	Remote Similarity	NPC477761
0.6857	Remote Similarity	NPC477758
0.6857	Remote Similarity	NPC477760
0.6857	Remote Similarity	NPC477754
0.6835	Remote Similarity	NPC142111
0.6835	Remote Similarity	NPC473315
0.6829	Remote Similarity	NPC471756
0.6829	Remote Similarity	NPC471755
0.6829	Remote Similarity	NPC137368
0.6812	Remote Similarity	NPC12040
0.6812	Remote Similarity	NPC471761
0.6812	Remote Similarity	NPC190418
0.6812	Remote Similarity	NPC76881
0.6812	Remote Similarity	NPC471760
0.6795	Remote Similarity	NPC21693
0.6795	Remote Similarity	NPC236649
0.6795	Remote Similarity	NPC469469
0.679	Remote Similarity	NPC470836
0.6765	Remote Similarity	NPC268243
0.675	Remote Similarity	NPC473308
0.6747	Remote Similarity	NPC104129
0.6747	Remote Similarity	NPC249408
0.6707	Remote Similarity	NPC475186
0.6707	Remote Similarity	NPC125142
0.6707	Remote Similarity	NPC118077
0.6707	Remote Similarity	NPC475037
0.6667	Remote Similarity	NPC6848
0.6667	Remote Similarity	NPC314821
0.6667	Remote Similarity	NPC317501
0.6667	Remote Similarity	NPC34581
0.6667	Remote Similarity	NPC327253
0.6667	Remote Similarity	NPC117596
0.6667	Remote Similarity	NPC118078
0.6667	Remote Similarity	NPC317626
0.6627	Remote Similarity	NPC248312
0.6627	Remote Similarity	NPC148534
0.6625	Remote Similarity	NPC473500
0.6625	Remote Similarity	NPC38295
0.6625	Remote Similarity	NPC470313
0.6625	Remote Similarity	NPC156089
0.662	Remote Similarity	NPC206601
0.6607	Remote Similarity	NPC266553
0.6588	Remote Similarity	NPC472124
0.6588	Remote Similarity	NPC472125
0.6588	Remote Similarity	NPC472199
0.6588	Remote Similarity	NPC472126
0.6588	Remote Similarity	NPC472197
0.6588	Remote Similarity	NPC9447
0.6585	Remote Similarity	NPC149018
0.6585	Remote Similarity	NPC171484
0.6585	Remote Similarity	NPC208473
0.6552	Remote Similarity	NPC29721
0.6548	Remote Similarity	NPC477748
0.6548	Remote Similarity	NPC50464
0.6548	Remote Similarity	NPC22918
0.6548	Remote Similarity	NPC285588
0.6543	Remote Similarity	NPC166279
0.6543	Remote Similarity	NPC288471
0.6538	Remote Similarity	NPC179933
0.6528	Remote Similarity	NPC250619
0.6528	Remote Similarity	NPC50228
0.6528	Remote Similarity	NPC97736
0.6528	Remote Similarity	NPC67099
0.6512	Remote Similarity	NPC472196
0.6512	Remote Similarity	NPC61201
0.6512	Remote Similarity	NPC320552
0.6512	Remote Similarity	NPC238090
0.6512	Remote Similarity	NPC472195
0.6506	Remote Similarity	NPC258501
0.6486	Remote Similarity	NPC184550
0.6486	Remote Similarity	NPC185419
0.6471	Remote Similarity	NPC470573
0.6471	Remote Similarity	NPC120021
0.6471	Remote Similarity	NPC202886
0.6471	Remote Similarity	NPC303451
0.6471	Remote Similarity	NPC6414
0.6471	Remote Similarity	NPC270908
0.6471	Remote Similarity	NPC216826
0.6471	Remote Similarity	NPC307699
0.6471	Remote Similarity	NPC231710
0.6471	Remote Similarity	NPC65665
0.6463	Remote Similarity	NPC475034
0.6438	Remote Similarity	NPC241265
0.6438	Remote Similarity	NPC211428
0.6438	Remote Similarity	NPC285003
0.6437	Remote Similarity	NPC159698
0.6437	Remote Similarity	NPC472198
0.6437	Remote Similarity	NPC72817
0.6437	Remote Similarity	NPC23454
0.6437	Remote Similarity	NPC70323
0.6437	Remote Similarity	NPC35269
0.6437	Remote Similarity	NPC477927
0.6437	Remote Similarity	NPC262312
0.6429	Remote Similarity	NPC470137
0.64	Remote Similarity	NPC291228
0.64	Remote Similarity	NPC308096
0.64	Remote Similarity	NPC143576
0.6395	Remote Similarity	NPC110072
0.6395	Remote Similarity	NPC302584
0.6395	Remote Similarity	NPC235051

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 NPC155457 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

range	Tanimoto Coefficient
0-0.1	203
0.1-0.2	4323
0.2-0.3	3331
0.3-0.4	913
0.4-0.5	289
0.5-0.6	55
0.6-0.7	16
0.7-0.8	18
0.8-0.85	2
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
0.807	Intermediate Similarity	NPD905	Approved
0.807	Intermediate Similarity	NPD904	Phase 3
0.7797	Intermediate Similarity	NPD892	Phase 3
0.7797	Intermediate Similarity	NPD889	Approved
0.7797	Intermediate Similarity	NPD888	Phase 3
0.7797	Intermediate Similarity	NPD891	Phase 3
0.7797	Intermediate Similarity	NPD894	Approved
0.7797	Intermediate Similarity	NPD890	Clinical (unspecified phase)
0.7797	Intermediate Similarity	NPD893	Approved
0.7797	Intermediate Similarity	NPD887	Approved
0.7797	Intermediate Similarity	NPD895	Approved
0.7627	Intermediate Similarity	NPD2269	Approved
0.75	Intermediate Similarity	NPD8999	Phase 3
0.75	Intermediate Similarity	NPD8993	Phase 1
0.75	Intermediate Similarity	NPD8997	Approved
0.75	Intermediate Similarity	NPD9000	Phase 3
0.75	Intermediate Similarity	NPD8998	Phase 2
0.7241	Intermediate Similarity	NPD8965	Approved
0.7241	Intermediate Similarity	NPD8966	Approved
0.7143	Intermediate Similarity	NPD2267	Suspended
0.697	Remote Similarity	NPD6123	Approved
0.6964	Remote Similarity	NPD8788	Approved
0.6765	Remote Similarity	NPD847	Phase 1
0.6667	Remote Similarity	NPD9035	Clinical (unspecified phase)
0.6667	Remote Similarity	NPD9036	Phase 3
0.6562	Remote Similarity	NPD7346	Approved
0.6552	Remote Similarity	NPD9006	Approved
0.6515	Remote Similarity	NPD369	Approved
0.6429	Remote Similarity	NPD1457	Discontinued
0.6389	Remote Similarity	NPD898	Approved
0.6389	Remote Similarity	NPD897	Approved
0.6389	Remote Similarity	NPD896	Approved
0.6167	Remote Similarity	NPD9219	Approved
0.6167	Remote Similarity	NPD9218	Clinical (unspecified phase)
0.6092	Remote Similarity	NPD8522	Clinical (unspecified phase)
0.6066	Remote Similarity	NPD8994	Approved
0.5974	Remote Similarity	NPD3181	Approved
0.597	Remote Similarity	NPD884	Clinical (unspecified phase)
0.597	Remote Similarity	NPD885	Approved
0.5921	Remote Similarity	NPD7532	Clinical (unspecified phase)
0.5833	Remote Similarity	NPD8958	Phase 2
0.5833	Remote Similarity	NPD8957	Approved
0.5833	Remote Similarity	NPD8961	Approved
0.5789	Remote Similarity	NPD9445	Approved
0.5758	Remote Similarity	NPD9050	Approved
0.5758	Remote Similarity	NPD9049	Discontinued
0.5732	Remote Similarity	NPD7329	Approved
0.573	Remote Similarity	NPD6698	Approved
0.573	Remote Similarity	NPD46	Approved
0.5714	Remote Similarity	NPD9052	Approved
0.5714	Remote Similarity	NPD9053	Approved
0.5714	Remote Similarity	NPD9051	Approved
0.5696	Remote Similarity	NPD1811	Approved
0.5696	Remote Similarity	NPD1810	Approved
0.5606	Remote Similarity	NPD1399	Approved
0.5606	Remote Similarity	NPD1400	Approved
0.56	Remote Similarity	NPD9032	Approved
0.56	Remote Similarity	NPD9030	Approved
0.56	Remote Similarity	NPD9031	Approved
0.56	Remote Similarity	NPD9033	Approved

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