Structure

Physi-Chem Properties

Molecular Weight:  416.22
Volume:  428.993
LogP:  3.276
LogD:  2.824
LogS:  -4.735
# Rotatable Bonds:  5
TPSA:  73.73
# H-Bond Aceptor:  6
# H-Bond Donor:  0
# Rings:  4
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.531
Synthetic Accessibility Score:  5.455
Fsp3:  0.625
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.639
MDCK Permeability:  1.77038546098629e-05
Pgp-inhibitor:  0.391
Pgp-substrate:  0.286
Human Intestinal Absorption (HIA):  0.006
20% Bioavailability (F20%):  0.004
30% Bioavailability (F30%):  0.219

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.474
Plasma Protein Binding (PPB):  91.24205017089844%
Volume Distribution (VD):  1.952
Pgp-substrate:  7.870149612426758%

ADMET: Metabolism

CYP1A2-inhibitor:  0.07
CYP1A2-substrate:  0.977
CYP2C19-inhibitor:  0.232
CYP2C19-substrate:  0.894
CYP2C9-inhibitor:  0.105
CYP2C9-substrate:  0.045
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.573
CYP3A4-inhibitor:  0.882
CYP3A4-substrate:  0.779

ADMET: Excretion

Clearance (CL):  4.224
Half-life (T1/2):  0.42

ADMET: Toxicity

hERG Blockers:  0.026
Human Hepatotoxicity (H-HT):  0.977
Drug-inuced Liver Injury (DILI):  0.896
AMES Toxicity:  0.687
Rat Oral Acute Toxicity:  0.777
Maximum Recommended Daily Dose:  0.389
Skin Sensitization:  0.811
Carcinogencity:  0.337
Eye Corrosion:  0.004
Eye Irritation:  0.123
Respiratory Toxicity:  0.978

Download Data

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

  Natural Product: NPC271632

Natural Product ID:  NPC271632
Common Name*:   Verrucosidin
IUPAC Name:   4-methoxy-3,5-dimethyl-6-[(2R,3S)-2-methyl-3-[(2E,4E)-4-methyl-5-[(1R,2R,4S,5S)-1,2,4-trimethyl-3,6-dioxabicyclo[3.1.0]hexan-4-yl]penta-2,4-dien-2-yl]oxiran-2-yl]pyran-2-one
Synonyms:   Verrucosidin
Standard InCHIKey:  JSVLNARHSWZARV-FOOXNAEUSA-N
Standard InCHI:  InChI=1S/C24H32O6/c1-12(11-22(6)21-23(7,30-21)16(5)28-22)10-13(2)18-24(8,29-18)19-14(3)17(26-9)15(4)20(25)27-19/h10-11,16,18,21H,1-9H3/b12-11+,13-10+/t16-,18+,21+,22+,23-,24-/m1/s1
SMILES:  COc1c(C)c(oc(=O)c1C)[C@]1(C)O[C@H]1/C(=C/C(=C/[C@]1(C)O[C@@H]([C@@]2([C@H]1O2)C)C)/C)/C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL512656
PubChem CID:   6437365
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000086] Pyrans
        • [CHEMONTID:0000481] Pyranones and derivatives

*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
NPO17126 Callicarpa pilosissima Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19193025]
NPO8921 Senna obtusifolia Species Fabaceae Eukaryota Seeds n.a. n.a. PMID[2213033]
NPO14849 Fritillaria unibracteata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19319 Cedrelopsis grevei Species Rutaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19725 Garcinia vilersiana Species Clusiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO23289.1 Heracleum sphondylium subsp. pyrenaicum Subspecies Apiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14849 Fritillaria unibracteata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO8921 Senna obtusifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19255 Necturus maculosus Species Proteidae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19319 Cedrelopsis grevei Species Rutaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO14849 Fritillaria unibracteata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO14849 Fritillaria unibracteata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO8921 Senna obtusifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19954 Conogethes punctiferalis Species Crambidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2988 Peteravenia schultzii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO36 Kleinia articulata Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO23289.1 Heracleum sphondylium subsp. pyrenaicum Subspecies Apiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18943 Dorstenia excentrica Species Moraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13440 Enterolobium cyclocarpum Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19529 Astrotrichilia asterotricha Species Meliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22955 Ranunculus lanuginosus Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17981 Melolontha vulgaris Species Scarabaeidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO16824 Cryptocarya oubatchensis Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19194 Licaria rigida Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19319 Cedrelopsis grevei Species Rutaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19452 Gaillardia pinnatifida Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19255 Necturus maculosus Species Proteidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO18452 Haplophyton cimicidum Species Apocynaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO14849 Fritillaria unibracteata Species Liliaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1884 Ptychodera flava Species Ptychoderidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO22603 Synedrellopsis grisebachii n.a. n.a. n.a. n.a. n.a. n.a. Database[UNPD]
NPO10435 Aphis serpylli Species Aphididae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO17126 Callicarpa pilosissima Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8921 Senna obtusifolia Species Fabaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19725 Garcinia vilersiana Species Clusiaceae 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

Target ID Target Type Target Name Target Organism Activity Type Activity Relation Value Unit Reference
NPT32 Organism Mus musculus Mus musculus LD50 = 4.0 mg.kg-1 PMID[538001]

☑ 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 NPC271632 and all remaining natural products in the NPASS database.
●  The right table: Most similar natural products (Tc>=0.56 or Top200).

Similarity Score Similarity Level Natural Product ID
0.7654 Intermediate Similarity NPC301525
0.76 Intermediate Similarity NPC308457
0.75 Intermediate Similarity NPC220766
0.75 Intermediate Similarity NPC476589
0.7447 Intermediate Similarity NPC124181
0.7436 Intermediate Similarity NPC276290
0.7407 Intermediate Similarity NPC107654
0.7407 Intermediate Similarity NPC470686
0.7403 Intermediate Similarity NPC124586
0.7403 Intermediate Similarity NPC191233
0.7381 Intermediate Similarity NPC471537
0.7349 Intermediate Similarity NPC471225
0.7349 Intermediate Similarity NPC68156
0.7342 Intermediate Similarity NPC470693
0.734 Intermediate Similarity NPC153559
0.7333 Intermediate Similarity NPC15193
0.7284 Intermediate Similarity NPC222244
0.7284 Intermediate Similarity NPC287878
0.7284 Intermediate Similarity NPC16349
0.7263 Intermediate Similarity NPC473307
0.7253 Intermediate Similarity NPC51653
0.725 Intermediate Similarity NPC59558
0.725 Intermediate Similarity NPC315285
0.725 Intermediate Similarity NPC64234
0.725 Intermediate Similarity NPC37929
0.7237 Intermediate Similarity NPC217940
0.7215 Intermediate Similarity NPC238223
0.7209 Intermediate Similarity NPC474894
0.72 Intermediate Similarity NPC26223
0.7195 Intermediate Similarity NPC474758
0.7195 Intermediate Similarity NPC315843
0.7191 Intermediate Similarity NPC61527
0.716 Intermediate Similarity NPC316185
0.7143 Intermediate Similarity NPC315394
0.7143 Intermediate Similarity NPC148233
0.7143 Intermediate Similarity NPC25747
0.7143 Intermediate Similarity NPC473825
0.7128 Intermediate Similarity NPC241407
0.7128 Intermediate Similarity NPC291709
0.7126 Intermediate Similarity NPC10080
0.7126 Intermediate Similarity NPC123908
0.7125 Intermediate Similarity NPC88877
0.7125 Intermediate Similarity NPC232812
0.7125 Intermediate Similarity NPC476591
0.7125 Intermediate Similarity NPC329656
0.7097 Intermediate Similarity NPC282644
0.7097 Intermediate Similarity NPC29798
0.7089 Intermediate Similarity NPC203335
0.7089 Intermediate Similarity NPC194871
0.7089 Intermediate Similarity NPC132286
0.7083 Intermediate Similarity NPC90819
0.7059 Intermediate Similarity NPC474005
0.7051 Intermediate Similarity NPC471556
0.7051 Intermediate Similarity NPC182794
0.7045 Intermediate Similarity NPC44261
0.7037 Intermediate Similarity NPC315597
0.7037 Intermediate Similarity NPC329904
0.7037 Intermediate Similarity NPC469660
0.7037 Intermediate Similarity NPC473361
0.7011 Intermediate Similarity NPC141810
0.7 Intermediate Similarity NPC470256
0.7 Intermediate Similarity NPC291712
0.6988 Remote Similarity NPC476355
0.6988 Remote Similarity NPC140287
0.6977 Remote Similarity NPC473980
0.6977 Remote Similarity NPC473981
0.6977 Remote Similarity NPC471299
0.6966 Remote Similarity NPC78673
0.6966 Remote Similarity NPC160517
0.6966 Remote Similarity NPC186155
0.6962 Remote Similarity NPC315115
0.6957 Remote Similarity NPC64913
0.6957 Remote Similarity NPC242877
0.6951 Remote Similarity NPC133098
0.6951 Remote Similarity NPC477084
0.6941 Remote Similarity NPC474278
0.6941 Remote Similarity NPC97516
0.6939 Remote Similarity NPC219038
0.6932 Remote Similarity NPC474028
0.6932 Remote Similarity NPC474439
0.6932 Remote Similarity NPC475690
0.6923 Remote Similarity NPC266957
0.6914 Remote Similarity NPC151481
0.6897 Remote Similarity NPC474739
0.6889 Remote Similarity NPC281172
0.6889 Remote Similarity NPC130030
0.6882 Remote Similarity NPC475748
0.6875 Remote Similarity NPC472266
0.6875 Remote Similarity NPC21998
0.6869 Remote Similarity NPC471599
0.686 Remote Similarity NPC474816
0.686 Remote Similarity NPC475699
0.686 Remote Similarity NPC23187
0.686 Remote Similarity NPC209135
0.686 Remote Similarity NPC279532
0.6854 Remote Similarity NPC16488
0.6854 Remote Similarity NPC475714
0.6854 Remote Similarity NPC170377
0.6854 Remote Similarity NPC170286
0.6854 Remote Similarity NPC475947
0.6854 Remote Similarity NPC315559
0.6848 Remote Similarity NPC233997
0.6848 Remote Similarity NPC260343
0.6842 Remote Similarity NPC471147
0.6842 Remote Similarity NPC133600
0.6835 Remote Similarity NPC282760
0.6835 Remote Similarity NPC471565
0.6835 Remote Similarity NPC471566
0.6829 Remote Similarity NPC316029
0.6824 Remote Similarity NPC123360
0.6824 Remote Similarity NPC470705
0.6818 Remote Similarity NPC475481
0.6818 Remote Similarity NPC79277
0.6813 Remote Similarity NPC204048
0.6813 Remote Similarity NPC186332
0.6813 Remote Similarity NPC47220
0.6809 Remote Similarity NPC32552
0.6809 Remote Similarity NPC32494
0.6809 Remote Similarity NPC175842
0.6804 Remote Similarity NPC471490
0.6795 Remote Similarity NPC179087
0.6795 Remote Similarity NPC210303
0.6795 Remote Similarity NPC44343
0.679 Remote Similarity NPC475760
0.679 Remote Similarity NPC313444
0.679 Remote Similarity NPC477117
0.6786 Remote Similarity NPC474280
0.6782 Remote Similarity NPC99651
0.6782 Remote Similarity NPC270126
0.6782 Remote Similarity NPC617
0.6782 Remote Similarity NPC475210
0.6778 Remote Similarity NPC475706
0.6774 Remote Similarity NPC133450
0.6774 Remote Similarity NPC95364
0.6774 Remote Similarity NPC83423
0.6774 Remote Similarity NPC142159
0.6771 Remote Similarity NPC471492
0.6753 Remote Similarity NPC127824
0.6753 Remote Similarity NPC79756
0.6753 Remote Similarity NPC309408
0.675 Remote Similarity NPC248125
0.675 Remote Similarity NPC146811
0.6747 Remote Similarity NPC163003
0.6744 Remote Similarity NPC49302
0.6744 Remote Similarity NPC141789
0.6744 Remote Similarity NPC171204
0.6744 Remote Similarity NPC474818
0.6744 Remote Similarity NPC262747
0.6744 Remote Similarity NPC51809
0.6744 Remote Similarity NPC176329
0.6744 Remote Similarity NPC125365
0.6744 Remote Similarity NPC476028
0.6742 Remote Similarity NPC475936
0.6742 Remote Similarity NPC474252
0.6742 Remote Similarity NPC313677
0.6739 Remote Similarity NPC231889
0.6739 Remote Similarity NPC475087
0.6739 Remote Similarity NPC476600
0.6737 Remote Similarity NPC189651
0.6737 Remote Similarity NPC165383
0.6737 Remote Similarity NPC475098
0.6737 Remote Similarity NPC248193
0.6737 Remote Similarity NPC59646
0.6735 Remote Similarity NPC151093
0.6733 Remote Similarity NPC477510
0.6733 Remote Similarity NPC471143
0.6709 Remote Similarity NPC477457
0.6709 Remote Similarity NPC477456
0.6707 Remote Similarity NPC269841
0.6707 Remote Similarity NPC473603
0.6707 Remote Similarity NPC476059
0.6706 Remote Similarity NPC469414
0.6706 Remote Similarity NPC329826
0.6706 Remote Similarity NPC478194
0.6706 Remote Similarity NPC315552
0.6706 Remote Similarity NPC478192
0.6706 Remote Similarity NPC478191
0.6706 Remote Similarity NPC478193
0.6706 Remote Similarity NPC329852
0.6706 Remote Similarity NPC478195
0.6706 Remote Similarity NPC478196
0.6705 Remote Similarity NPC281132
0.6703 Remote Similarity NPC471223
0.6703 Remote Similarity NPC67081
0.6703 Remote Similarity NPC474424
0.6703 Remote Similarity NPC197903
0.6703 Remote Similarity NPC474547
0.6703 Remote Similarity NPC99395
0.6702 Remote Similarity NPC327253
0.6702 Remote Similarity NPC3436
0.6702 Remote Similarity NPC177668
0.6702 Remote Similarity NPC3952
0.6701 Remote Similarity NPC473333
0.6667 Remote Similarity NPC108045
0.6667 Remote Similarity NPC477512
0.6667 Remote Similarity NPC474193
0.6667 Remote Similarity NPC473471
0.6667 Remote Similarity NPC108816
0.6667 Remote Similarity NPC473658
0.6667 Remote Similarity NPC244878

  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 NPC271632 and all drugs/candidates.
●  The right table: Most similar clinical/approved drugs (Tc>=0.56 or Top200).

Similarity Score Similarity Level Drug ID Developmental Stage
0.7273 Intermediate Similarity NPD2685 Clinical (unspecified phase)
0.6882 Remote Similarity NPD7838 Discovery
0.6837 Remote Similarity NPD6648 Approved
0.6702 Remote Similarity NPD46 Approved
0.6702 Remote Similarity NPD6698 Approved
0.6593 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6556 Remote Similarity NPD5209 Approved
0.6522 Remote Similarity NPD1733 Clinical (unspecified phase)
0.6436 Remote Similarity NPD5344 Discontinued
0.6296 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6238 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6216 Remote Similarity NPD6927 Phase 3
0.6136 Remote Similarity NPD8039 Approved
0.6129 Remote Similarity NPD7154 Phase 3
0.6078 Remote Similarity NPD4225 Approved
0.6042 Remote Similarity NPD1282 Approved
0.5918 Remote Similarity NPD1695 Approved
0.5876 Remote Similarity NPD4251 Approved
0.5876 Remote Similarity NPD4250 Approved
0.5875 Remote Similarity NPD585 Clinical (unspecified phase)
0.5851 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5833 Remote Similarity NPD7899 Clinical (unspecified phase)
0.5824 Remote Similarity NPD4756 Discovery
0.5818 Remote Similarity NPD2067 Discontinued
0.5806 Remote Similarity NPD5790 Clinical (unspecified phase)
0.58 Remote Similarity NPD7983 Approved
0.58 Remote Similarity NPD7637 Suspended
0.5789 Remote Similarity NPD6110 Phase 1
0.5789 Remote Similarity NPD7115 Discovery
0.5773 Remote Similarity NPD4249 Approved
0.575 Remote Similarity NPD8779 Phase 3
0.5714 Remote Similarity NPD6053 Discontinued
0.5688 Remote Similarity NPD5954 Clinical (unspecified phase)
0.5676 Remote Similarity NPD6371 Approved
0.567 Remote Similarity NPD1694 Approved
0.567 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5638 Remote Similarity NPD4819 Approved
0.5638 Remote Similarity NPD4820 Approved
0.5638 Remote Similarity NPD4821 Approved
0.5638 Remote Similarity NPD4822 Approved
0.5625 Remote Similarity NPD8413 Clinical (unspecified phase)
0.56 Remote Similarity NPD6051 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