Structure

Physi-Chem Properties

Molecular Weight:  332.25
Volume:  366.391
LogP:  3.843
LogD:  3.803
LogS:  -3.406
# Rotatable Bonds:  7
TPSA:  65.12
# H-Bond Aceptor:  4
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.515
Synthetic Accessibility Score:  4.471
Fsp3:  0.65
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.813
MDCK Permeability:  8.613727914053015e-06
Pgp-inhibitor:  0.001
Pgp-substrate:  0.068
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.023
30% Bioavailability (F30%):  0.014

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.432
Plasma Protein Binding (PPB):  94.84481048583984%
Volume Distribution (VD):  0.878
Pgp-substrate:  5.006774425506592%

ADMET: Metabolism

CYP1A2-inhibitor:  0.167
CYP1A2-substrate:  0.865
CYP2C19-inhibitor:  0.801
CYP2C19-substrate:  0.707
CYP2C9-inhibitor:  0.343
CYP2C9-substrate:  0.904
CYP2D6-inhibitor:  0.036
CYP2D6-substrate:  0.528
CYP3A4-inhibitor:  0.602
CYP3A4-substrate:  0.169

ADMET: Excretion

Clearance (CL):  11.697
Half-life (T1/2):  0.449

ADMET: Toxicity

hERG Blockers:  0.027
Human Hepatotoxicity (H-HT):  0.329
Drug-inuced Liver Injury (DILI):  0.071
AMES Toxicity:  0.013
Rat Oral Acute Toxicity:  0.099
Maximum Recommended Daily Dose:  0.214
Skin Sensitization:  0.814
Carcinogencity:  0.154
Eye Corrosion:  0.009
Eye Irritation:  0.118
Respiratory Toxicity:  0.885

Download Data

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

  Natural Product: NPC224072

Natural Product ID:  NPC224072
Common Name*:   Sollasin B
IUPAC Name:   (E)-3-methyl-N-[(3R)-2-oxopiperidin-3-yl]-5-[(1S,6R)-1,2,6-trimethylcyclohex-2-en-1-yl]pent-2-enamide
Synonyms:  
Standard InCHIKey:  AETOKBXKVBFSTR-VBRACAIISA-N
Standard InCHI:  InChI=1S/C20H32N2O2/c1-14(10-11-20(4)15(2)7-5-8-16(20)3)13-18(23)22-17-9-6-12-21-19(17)24/h7,13,16-17H,5-6,8-12H2,1-4H3,(H,21,24)(H,22,23)/b14-13+/t16-,17-,20-/m1/s1
SMILES:  C/C(=CC(=N[C@@H]1CCCN=C1O)O)/CC[C@@]1(C)[C@H](C)CCC=C1C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL483421
PubChem CID:   44575909
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0001189] N-acyl-alpha amino acids 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
NPO8264 Holothuria scabra Species Holothuriidae Eukaryota n.a. n.a. n.a. PMID[18087805]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. whole plant n.a. PMID[28294414]
NPO4135 Poecillastra sollasi Species Vulcanellidae Eukaryota n.a. n.a. n.a. PMID[8496702]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota Fruit n.a. n.a. Database[FooDB]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. Database[FooDB]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO7239 Gnetum parvifolium Species Gnetaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO7239 Gnetum parvifolium Species Gnetaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO1304 Macrozamia macdonnelli Species Zamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO4135 Poecillastra sollasi Species Vulcanellidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO3550 Clerodendrum phlomidis Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO13199 Syzygium jambos Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO7239 Gnetum parvifolium Species Gnetaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO5112 Adonis leiosepala Species Ranunculaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO21035 Crinum oliganthum Species Amaryllidaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO606 Felicia filifolia Species Asteraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2032 Eucalyptus aggregata Species Myrtaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO2227 Clerodendrum splendens Species Lamiaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8264 Holothuria scabra Species Holothuriidae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO8799 Quassia multiflora Species Simaroubaceae 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
NPT168 Cell Line P388 Mus musculus IC50 = 6.0 ug.mL-1 PMID[541500]
NPT81 Cell Line A549 Homo sapiens IC50 = 17.0 ug.mL-1 PMID[541500]
NPT20 Organism Candida albicans Candida albicans MIC = 125.0 ug.mL-1 PMID[541500]
NPT85 Organism Filobasidiella neoformans Cryptococcus neoformans MIC = 31.2 ug.mL-1 PMID[541500]

☑ 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 NPC224072 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
0.9 High Similarity NPC39966
0.7727 Intermediate Similarity NPC166458
0.7556 Intermediate Similarity NPC316186
0.7556 Intermediate Similarity NPC34754
0.7347 Intermediate Similarity NPC471083
0.7347 Intermediate Similarity NPC247060
0.7347 Intermediate Similarity NPC50815
0.7222 Intermediate Similarity NPC152684
0.7113 Intermediate Similarity NPC240650
0.71 Intermediate Similarity NPC45365
0.71 Intermediate Similarity NPC90538
0.71 Intermediate Similarity NPC293299
0.6979 Remote Similarity NPC243985
0.6979 Remote Similarity NPC280710
0.6961 Remote Similarity NPC55462
0.6939 Remote Similarity NPC4834
0.6931 Remote Similarity NPC474583
0.6835 Remote Similarity NPC29468
0.6832 Remote Similarity NPC152718
0.6832 Remote Similarity NPC226509
0.68 Remote Similarity NPC275686
0.6778 Remote Similarity NPC475724
0.6778 Remote Similarity NPC257962
0.6768 Remote Similarity NPC167419
0.6699 Remote Similarity NPC469958
0.6698 Remote Similarity NPC472359
0.6633 Remote Similarity NPC473314
0.6602 Remote Similarity NPC474563
0.6571 Remote Similarity NPC25340
0.65 Remote Similarity NPC130807
0.6476 Remote Similarity NPC230677
0.6465 Remote Similarity NPC477290
0.6458 Remote Similarity NPC324405
0.6449 Remote Similarity NPC175585
0.6429 Remote Similarity NPC69649
0.6429 Remote Similarity NPC68703
0.6422 Remote Similarity NPC56796
0.6422 Remote Similarity NPC80834
0.6422 Remote Similarity NPC469968
0.6404 Remote Similarity NPC476308
0.6395 Remote Similarity NPC34834
0.6392 Remote Similarity NPC249312
0.6386 Remote Similarity NPC477525
0.6355 Remote Similarity NPC140251
0.6355 Remote Similarity NPC307903
0.6337 Remote Similarity NPC475503
0.6321 Remote Similarity NPC258130
0.631 Remote Similarity NPC279434
0.6296 Remote Similarity NPC311809
0.6279 Remote Similarity NPC45060
0.6279 Remote Similarity NPC280065
0.6279 Remote Similarity NPC103712
0.6279 Remote Similarity NPC291196
0.6275 Remote Similarity NPC475646
0.6235 Remote Similarity NPC114651
0.622 Remote Similarity NPC124849
0.622 Remote Similarity NPC21848
0.6211 Remote Similarity NPC477199
0.6203 Remote Similarity NPC261158
0.6203 Remote Similarity NPC104138
0.6203 Remote Similarity NPC24216
0.6203 Remote Similarity NPC306420
0.6196 Remote Similarity NPC471597
0.6176 Remote Similarity NPC476903
0.6176 Remote Similarity NPC247220
0.6173 Remote Similarity NPC312826
0.617 Remote Similarity NPC283277
0.6145 Remote Similarity NPC81615
0.6136 Remote Similarity NPC265789
0.6136 Remote Similarity NPC476329
0.6136 Remote Similarity NPC21773
0.6129 Remote Similarity NPC476560
0.6125 Remote Similarity NPC11130
0.6121 Remote Similarity NPC242692
0.6118 Remote Similarity NPC242945
0.6118 Remote Similarity NPC37792
0.6118 Remote Similarity NPC259156
0.6111 Remote Similarity NPC69383
0.6111 Remote Similarity NPC169375
0.6111 Remote Similarity NPC313179
0.6111 Remote Similarity NPC171148
0.6105 Remote Similarity NPC477584
0.6098 Remote Similarity NPC309877
0.6092 Remote Similarity NPC473893
0.6092 Remote Similarity NPC471560
0.6092 Remote Similarity NPC472831
0.6092 Remote Similarity NPC138409
0.6091 Remote Similarity NPC476290
0.6087 Remote Similarity NPC469492
0.6078 Remote Similarity NPC272732
0.6078 Remote Similarity NPC303045
0.6078 Remote Similarity NPC161972
0.6078 Remote Similarity NPC311164
0.6076 Remote Similarity NPC471992
0.6076 Remote Similarity NPC297020
0.6076 Remote Similarity NPC273023
0.6075 Remote Similarity NPC119329
0.6071 Remote Similarity NPC476682
0.6068 Remote Similarity NPC472458
0.6068 Remote Similarity NPC469943
0.6058 Remote Similarity NPC140685
0.6047 Remote Similarity NPC171225
0.6024 Remote Similarity NPC469728
0.6024 Remote Similarity NPC219621
0.6023 Remote Similarity NPC189745
0.6022 Remote Similarity NPC469517
0.6019 Remote Similarity NPC36497
0.6 Remote Similarity NPC306727
0.6 Remote Similarity NPC107258
0.6 Remote Similarity NPC476904
0.6 Remote Similarity NPC476366
0.6 Remote Similarity NPC474964
0.6 Remote Similarity NPC288086
0.6 Remote Similarity NPC201048
0.6 Remote Similarity NPC477288
0.6 Remote Similarity NPC215474
0.5982 Remote Similarity NPC476269
0.5979 Remote Similarity NPC75810
0.5979 Remote Similarity NPC24733
0.5978 Remote Similarity NPC91594
0.5977 Remote Similarity NPC249713
0.5976 Remote Similarity NPC325550
0.5976 Remote Similarity NPC329003
0.5976 Remote Similarity NPC326524
0.5963 Remote Similarity NPC475800
0.5962 Remote Similarity NPC140300
0.5952 Remote Similarity NPC174956
0.5946 Remote Similarity NPC328052
0.5946 Remote Similarity NPC122926
0.5946 Remote Similarity NPC113012
0.5943 Remote Similarity NPC77703
0.5943 Remote Similarity NPC469457
0.5941 Remote Similarity NPC476064
0.5934 Remote Similarity NPC32832
0.5934 Remote Similarity NPC125828
0.593 Remote Similarity NPC286669
0.593 Remote Similarity NPC476039
0.593 Remote Similarity NPC222366
0.5918 Remote Similarity NPC474458
0.5917 Remote Similarity NPC237286
0.5914 Remote Similarity NPC476314
0.5914 Remote Similarity NPC83351
0.5914 Remote Similarity NPC167891
0.5909 Remote Similarity NPC474248
0.5909 Remote Similarity NPC159367
0.5904 Remote Similarity NPC176621
0.5893 Remote Similarity NPC66862
0.5889 Remote Similarity NPC314678
0.5889 Remote Similarity NPC474743
0.5889 Remote Similarity NPC130665
0.5888 Remote Similarity NPC469598
0.5882 Remote Similarity NPC290367
0.5882 Remote Similarity NPC107540
0.5875 Remote Similarity NPC242930
0.587 Remote Similarity NPC244488
0.587 Remote Similarity NPC247325
0.587 Remote Similarity NPC265588
0.587 Remote Similarity NPC253190
0.587 Remote Similarity NPC470749
0.587 Remote Similarity NPC7214
0.5865 Remote Similarity NPC25565
0.5865 Remote Similarity NPC476449
0.5862 Remote Similarity NPC197805
0.5856 Remote Similarity NPC474725
0.5854 Remote Similarity NPC321030
0.5854 Remote Similarity NPC210999
0.5851 Remote Similarity NPC30986
0.5851 Remote Similarity NPC81306
0.5851 Remote Similarity NPC47982
0.5851 Remote Similarity NPC109546
0.5851 Remote Similarity NPC143182
0.5851 Remote Similarity NPC84694
0.5851 Remote Similarity NPC28862
0.5851 Remote Similarity NPC209430
0.5833 Remote Similarity NPC241879
0.5833 Remote Similarity NPC210346
0.5833 Remote Similarity NPC477583
0.5833 Remote Similarity NPC41160
0.5833 Remote Similarity NPC473254
0.5826 Remote Similarity NPC288629
0.5825 Remote Similarity NPC116930
0.5823 Remote Similarity NPC303672
0.5814 Remote Similarity NPC163678
0.581 Remote Similarity NPC474164
0.581 Remote Similarity NPC473501
0.581 Remote Similarity NPC311242
0.581 Remote Similarity NPC475439
0.5806 Remote Similarity NPC470711
0.5806 Remote Similarity NPC132542
0.5806 Remote Similarity NPC470758
0.5804 Remote Similarity NPC72753
0.5802 Remote Similarity NPC4881
0.5795 Remote Similarity NPC216460
0.5795 Remote Similarity NPC208999
0.5795 Remote Similarity NPC96484
0.5794 Remote Similarity NPC118275
0.5789 Remote Similarity NPC87359
0.5789 Remote Similarity NPC180402
0.5789 Remote Similarity NPC96362
0.5789 Remote Similarity NPC234193

  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 NPC224072 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
0.7717 Intermediate Similarity NPD5771 Approved
0.6867 Remote Similarity NPD791 Approved
0.6867 Remote Similarity NPD15 Approved
0.6804 Remote Similarity NPD5769 Clinical (unspecified phase)
0.6782 Remote Similarity NPD1346 Approved
0.6471 Remote Similarity NPD1082 Approved
0.6311 Remote Similarity NPD6404 Discontinued
0.622 Remote Similarity NPD835 Approved
0.622 Remote Similarity NPD834 Approved
0.6207 Remote Similarity NPD6939 Phase 2
0.6207 Remote Similarity NPD6938 Clinical (unspecified phase)
0.6173 Remote Similarity NPD571 Approved
0.6145 Remote Similarity NPD832 Approved
0.6145 Remote Similarity NPD833 Approved
0.6122 Remote Similarity NPD4722 Approved
0.6122 Remote Similarity NPD4723 Approved
0.6111 Remote Similarity NPD8264 Approved
0.6049 Remote Similarity NPD570 Approved
0.5842 Remote Similarity NPD4001 Clinical (unspecified phase)
0.5842 Remote Similarity NPD790 Approved
0.5802 Remote Similarity NPD273 Approved
0.5794 Remote Similarity NPD4760 Clinical (unspecified phase)
0.5789 Remote Similarity NPD362 Phase 1
0.578 Remote Similarity NPD179 Clinical (unspecified phase)
0.5728 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5727 Remote Similarity NPD6640 Phase 3
0.5726 Remote Similarity NPD6914 Discontinued
0.561 Remote Similarity NPD4219 Approved
0.5604 Remote Similarity NPD4243 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