Structure

Physi-Chem Properties

Molecular Weight:  305.24
Volume:  346.655
LogP:  2.75
LogD:  2.881
LogS:  -2.592
# Rotatable Bonds:  8
TPSA:  29.54
# H-Bond Aceptor:  3
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  3

MedChem Properties

QED Drug-Likeness Score:  0.4
Synthetic Accessibility Score:  4.181
Fsp3:  0.632
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -4.587
MDCK Permeability:  3.341786577948369e-05
Pgp-inhibitor:  0.348
Pgp-substrate:  0.008
Human Intestinal Absorption (HIA):  0.032
20% Bioavailability (F20%):  0.304
30% Bioavailability (F30%):  0.722

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.596
Plasma Protein Binding (PPB):  64.67456817626953%
Volume Distribution (VD):  1.391
Pgp-substrate:  23.77226448059082%

ADMET: Metabolism

CYP1A2-inhibitor:  0.279
CYP1A2-substrate:  0.912
CYP2C19-inhibitor:  0.481
CYP2C19-substrate:  0.921
CYP2C9-inhibitor:  0.077
CYP2C9-substrate:  0.978
CYP2D6-inhibitor:  0.984
CYP2D6-substrate:  0.942
CYP3A4-inhibitor:  0.8
CYP3A4-substrate:  0.263

ADMET: Excretion

Clearance (CL):  2.337
Half-life (T1/2):  0.277

ADMET: Toxicity

hERG Blockers:  0.389
Human Hepatotoxicity (H-HT):  0.441
Drug-inuced Liver Injury (DILI):  0.616
AMES Toxicity:  0.284
Rat Oral Acute Toxicity:  0.048
Maximum Recommended Daily Dose:  0.894
Skin Sensitization:  0.943
Carcinogencity:  0.61
Eye Corrosion:  0.509
Eye Irritation:  0.394
Respiratory Toxicity:  0.953

Download Data

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

  Natural Product: NPC470993

Natural Product ID:  NPC470993
Common Name*:   Microgrewiapine C
IUPAC Name:   (2S,3S,6S)-6-[(1E,3E,5E)-deca-1,3,5-trienyl]-1,2-dimethyl-1-oxidopiperidin-1-ium-3-ol
Synonyms:   Microgrewiapine C
Standard InCHIKey:  LZZRCKFXUQNNGN-PZIHOPEQSA-N
Standard InCHI:  InChI=1S/C17H29NO2/c1-4-5-6-7-8-9-10-11-12-16-13-14-17(19)15(2)18(16,3)20/h7-12,15-17,19H,4-6,13-14H2,1-3H3/b8-7+,10-9+,12-11+/t15-,16+,17-,18?/m0/s1
SMILES:  CCCC/C=C/C=C/C=C/[C@@H]1CC[C@@H]([C@@H](N1(=O)C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2334870
PubChem CID:   71578972
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000195] Piperidines

*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
NPO2350 Microcos paniculata Species Malvaceae Eukaryota n.a. n.a. n.a. PMID[23327794]
NPO2350 Microcos paniculata Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO2350 Microcos paniculata Species Malvaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO2350 Microcos paniculata Species Malvaceae 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
NPT139 Cell Line HT-29 Homo sapiens IC50 > 10000.0 nM PMID[488885]
NPT409 Protein Complex Neuronal acetylcholine receptor; alpha4/beta2 Homo sapiens Inhibition = 67.3 % PMID[488885]
NPT411 Protein Complex Neuronal acetylcholine receptor; alpha3/beta4 Homo sapiens Inhibition = 82.8 % PMID[488885]

☑ 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 NPC470993 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
1.0 High Similarity NPC470992
0.9265 High Similarity NPC23721
0.8493 Intermediate Similarity NPC26932
0.7895 Intermediate Similarity NPC470994
0.7531 Intermediate Similarity NPC209232
0.7436 Intermediate Similarity NPC473588
0.7436 Intermediate Similarity NPC78562
0.7284 Intermediate Similarity NPC475363
0.7284 Intermediate Similarity NPC473971
0.7284 Intermediate Similarity NPC473972
0.6914 Remote Similarity NPC34672
0.68 Remote Similarity NPC477106
0.6782 Remote Similarity NPC475975
0.6667 Remote Similarity NPC47333
0.6538 Remote Similarity NPC113224
0.6512 Remote Similarity NPC476560
0.6486 Remote Similarity NPC233364
0.6486 Remote Similarity NPC471421
0.6471 Remote Similarity NPC473695
0.6471 Remote Similarity NPC473446
0.6421 Remote Similarity NPC25033
0.6421 Remote Similarity NPC119225
0.6421 Remote Similarity NPC476261
0.6421 Remote Similarity NPC471635
0.6421 Remote Similarity NPC470382
0.642 Remote Similarity NPC97614
0.6337 Remote Similarity NPC472856
0.6234 Remote Similarity NPC51166
0.6154 Remote Similarity NPC471419
0.6154 Remote Similarity NPC55068
0.6154 Remote Similarity NPC163134
0.6133 Remote Similarity NPC168308
0.6133 Remote Similarity NPC302569
0.6122 Remote Similarity NPC91036
0.6118 Remote Similarity NPC217095
0.6118 Remote Similarity NPC264417
0.6104 Remote Similarity NPC42477
0.6098 Remote Similarity NPC291196
0.6098 Remote Similarity NPC103712
0.6081 Remote Similarity NPC242930
0.6076 Remote Similarity NPC206660
0.6067 Remote Similarity NPC277341
0.6067 Remote Similarity NPC226982
0.6053 Remote Similarity NPC321030
0.6049 Remote Similarity NPC470663
0.6022 Remote Similarity NPC324506
0.6 Remote Similarity NPC477525
0.5974 Remote Similarity NPC325550
0.5974 Remote Similarity NPC329003
0.5974 Remote Similarity NPC326524
0.5949 Remote Similarity NPC471023
0.5941 Remote Similarity NPC100810
0.5941 Remote Similarity NPC144714
0.593 Remote Similarity NPC212008
0.593 Remote Similarity NPC51055
0.593 Remote Similarity NPC140327
0.593 Remote Similarity NPC3094
0.593 Remote Similarity NPC62293
0.5915 Remote Similarity NPC302310
0.5904 Remote Similarity NPC127145
0.5904 Remote Similarity NPC475930
0.5889 Remote Similarity NPC82799
0.5882 Remote Similarity NPC314678
0.5882 Remote Similarity NPC473289
0.5882 Remote Similarity NPC305223
0.5844 Remote Similarity NPC170172
0.5833 Remote Similarity NPC474674
0.5814 Remote Similarity NPC288086
0.5811 Remote Similarity NPC277072
0.5811 Remote Similarity NPC178263
0.5773 Remote Similarity NPC145707
0.5769 Remote Similarity NPC477001
0.5769 Remote Similarity NPC477000
0.5753 Remote Similarity NPC71053
0.5753 Remote Similarity NPC59408
0.5733 Remote Similarity NPC110732
0.5732 Remote Similarity NPC129995
0.5732 Remote Similarity NPC315141
0.5714 Remote Similarity NPC137620
0.5714 Remote Similarity NPC474675
0.5714 Remote Similarity NPC204709
0.57 Remote Similarity NPC289140
0.5679 Remote Similarity NPC233034
0.5673 Remote Similarity NPC473254
0.5673 Remote Similarity NPC55336
0.5667 Remote Similarity NPC471768
0.5647 Remote Similarity NPC476695
0.5647 Remote Similarity NPC476694
0.5647 Remote Similarity NPC476696
0.5647 Remote Similarity NPC324638
0.5647 Remote Similarity NPC306973
0.5647 Remote Similarity NPC470662
0.5625 Remote Similarity NPC29468
0.5625 Remote Similarity NPC316186
0.5619 Remote Similarity NPC75523
0.5604 Remote Similarity NPC79367
0.5604 Remote Similarity NPC207657

  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 NPC470993 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
0.6154 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6104 Remote Similarity NPD393 Approved
0.5974 Remote Similarity NPD9455 Approved
0.5823 Remote Similarity NPD6949 Clinical (unspecified phase)
0.5679 Remote Similarity NPD9440 Discontinued
0.5647 Remote Similarity NPD3212 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