Structure

Physi-Chem Properties

Molecular Weight:  263.22
Volume:  305.909
LogP:  2.289
LogD:  2.303
LogS:  -2.304
# Rotatable Bonds:  6
TPSA:  23.47
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.583
Synthetic Accessibility Score:  4.237
Fsp3:  0.647
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:  -4.565
MDCK Permeability:  3.723337431438267e-05
Pgp-inhibitor:  0.014
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.051
20% Bioavailability (F20%):  0.032
30% Bioavailability (F30%):  0.072

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.433
Plasma Protein Binding (PPB):  69.60115814208984%
Volume Distribution (VD):  1.51
Pgp-substrate:  24.792865753173828%

ADMET: Metabolism

CYP1A2-inhibitor:  0.241
CYP1A2-substrate:  0.955
CYP2C19-inhibitor:  0.41
CYP2C19-substrate:  0.932
CYP2C9-inhibitor:  0.052
CYP2C9-substrate:  0.981
CYP2D6-inhibitor:  0.973
CYP2D6-substrate:  0.952
CYP3A4-inhibitor:  0.08
CYP3A4-substrate:  0.213

ADMET: Excretion

Clearance (CL):  4.359
Half-life (T1/2):  0.283

ADMET: Toxicity

hERG Blockers:  0.439
Human Hepatotoxicity (H-HT):  0.358
Drug-inuced Liver Injury (DILI):  0.188
AMES Toxicity:  0.109
Rat Oral Acute Toxicity:  0.149
Maximum Recommended Daily Dose:  0.906
Skin Sensitization:  0.919
Carcinogencity:  0.447
Eye Corrosion:  0.544
Eye Irritation:  0.627
Respiratory Toxicity:  0.952

Download Data

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

  Natural Product: NPC23721

Natural Product ID:  NPC23721
Common Name*:   Microgrewiapine A
IUPAC Name:   (2S,3R,6S)-6-[(1E,3E,5E)-deca-1,3,5-trienyl]-1,2-dimethylpiperidin-3-ol
Synonyms:   Microgrewiapine A
Standard InCHIKey:  ZBJGGLXQNXXXRO-VCZRHBNQSA-N
Standard InCHI:  InChI=1S/C17H29NO/c1-4-5-6-7-8-9-10-11-12-16-13-14-17(19)15(2)18(16)3/h7-12,15-17,19H,4-6,13-14H2,1-3H3/b8-7+,10-9+,12-11+/t15-,16+,17+/m0/s1
SMILES:  CCCC/C=C/C=C/C=C/[C@@H]1CC[C@H]([C@H](C)N1C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2334868
PubChem CID:   71576920
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 = 6800.0 nM PMID[455095]
NPT27 Others Unspecified Ratio IC50 = 4.0 n.a. PMID[455095]
NPT27 Others Unspecified IC50 = 30400.0 nM PMID[455095]
NPT409 Protein Complex Neuronal acetylcholine receptor; alpha4/beta2 Homo sapiens Inhibition = 74.0 % PMID[455095]
NPT411 Protein Complex Neuronal acetylcholine receptor; alpha3/beta4 Homo sapiens Inhibition = 58.2 % PMID[455095]

☑ 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 NPC23721 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
0.9265 High Similarity NPC470992
0.9265 High Similarity NPC470993
0.9118 High Similarity NPC26932
0.8194 Intermediate Similarity NPC470994
0.7945 Intermediate Similarity NPC473588
0.7945 Intermediate Similarity NPC78562
0.7792 Intermediate Similarity NPC209232
0.7763 Intermediate Similarity NPC475363
0.7763 Intermediate Similarity NPC473971
0.7763 Intermediate Similarity NPC473972
0.7143 Intermediate Similarity NPC34672
0.7042 Intermediate Similarity NPC477106
0.6988 Remote Similarity NPC475975
0.6914 Remote Similarity NPC476560
0.6901 Remote Similarity NPC47333
0.6875 Remote Similarity NPC473446
0.6875 Remote Similarity NPC473695
0.6757 Remote Similarity NPC113224
0.6714 Remote Similarity NPC233364
0.6714 Remote Similarity NPC471421
0.6623 Remote Similarity NPC97614
0.6593 Remote Similarity NPC476261
0.6593 Remote Similarity NPC470382
0.6593 Remote Similarity NPC119225
0.6593 Remote Similarity NPC471635
0.6593 Remote Similarity NPC25033
0.6571 Remote Similarity NPC302569
0.6571 Remote Similarity NPC168308
0.6528 Remote Similarity NPC42477
0.6486 Remote Similarity NPC206660
0.6351 Remote Similarity NPC163134
0.6351 Remote Similarity NPC55068
0.6351 Remote Similarity NPC471419
0.6296 Remote Similarity NPC264417
0.6296 Remote Similarity NPC217095
0.6286 Remote Similarity NPC242930
0.6282 Remote Similarity NPC291196
0.6282 Remote Similarity NPC103712
0.6277 Remote Similarity NPC91036
0.625 Remote Similarity NPC321030
0.6235 Remote Similarity NPC226982
0.6235 Remote Similarity NPC277341
0.6232 Remote Similarity NPC178263
0.6232 Remote Similarity NPC277072
0.6184 Remote Similarity NPC477525
0.618 Remote Similarity NPC324506
0.6164 Remote Similarity NPC326524
0.6164 Remote Similarity NPC325550
0.6164 Remote Similarity NPC329003
0.6133 Remote Similarity NPC471023
0.6119 Remote Similarity NPC302310
0.6098 Remote Similarity NPC51055
0.6098 Remote Similarity NPC3094
0.6098 Remote Similarity NPC212008
0.6098 Remote Similarity NPC62293
0.6098 Remote Similarity NPC140327
0.6082 Remote Similarity NPC144714
0.6082 Remote Similarity NPC100810
0.6076 Remote Similarity NPC127145
0.6076 Remote Similarity NPC475930
0.6049 Remote Similarity NPC314678
0.6049 Remote Similarity NPC305223
0.6047 Remote Similarity NPC82799
0.6027 Remote Similarity NPC170172
0.602 Remote Similarity NPC473289
0.6 Remote Similarity NPC474674
0.5976 Remote Similarity NPC288086
0.596 Remote Similarity NPC473254
0.5942 Remote Similarity NPC59408
0.5942 Remote Similarity NPC71053
0.5915 Remote Similarity NPC110732
0.5914 Remote Similarity NPC145707
0.5909 Remote Similarity NPC276825
0.59 Remote Similarity NPC477001
0.59 Remote Similarity NPC477000
0.5897 Remote Similarity NPC129995
0.5897 Remote Similarity NPC315141
0.589 Remote Similarity NPC204709
0.5875 Remote Similarity NPC474675
0.5875 Remote Similarity NPC137620
0.5844 Remote Similarity NPC233034
0.5842 Remote Similarity NPC472856
0.5833 Remote Similarity NPC289140
0.5814 Remote Similarity NPC471768
0.5802 Remote Similarity NPC476694
0.5802 Remote Similarity NPC476696
0.5802 Remote Similarity NPC476695
0.5802 Remote Similarity NPC324638
0.5802 Remote Similarity NPC306973
0.58 Remote Similarity NPC55336
0.5789 Remote Similarity NPC252684
0.5789 Remote Similarity NPC29468
0.5761 Remote Similarity NPC316186
0.5758 Remote Similarity NPC214200
0.5758 Remote Similarity NPC228400
0.5753 Remote Similarity NPC471605
0.5753 Remote Similarity NPC471443
0.575 Remote Similarity NPC268922
0.575 Remote Similarity NPC474812
0.5747 Remote Similarity NPC79367
0.5747 Remote Similarity NPC207657
0.5733 Remote Similarity NPC133923
0.5729 Remote Similarity NPC272732
0.5729 Remote Similarity NPC311164
0.5728 Remote Similarity NPC159367
0.5714 Remote Similarity NPC281154
0.5714 Remote Similarity NPC91604
0.5714 Remote Similarity NPC315170
0.5698 Remote Similarity NPC474833
0.5694 Remote Similarity NPC471423
0.5694 Remote Similarity NPC471442
0.5679 Remote Similarity NPC471022
0.5672 Remote Similarity NPC76976
0.567 Remote Similarity NPC476903
0.5667 Remote Similarity NPC477199
0.5658 Remote Similarity NPC130807
0.5641 Remote Similarity NPC235311
0.5641 Remote Similarity NPC253468
0.5641 Remote Similarity NPC476559
0.5631 Remote Similarity NPC315426
0.5625 Remote Similarity NPC126664
0.5625 Remote Similarity NPC34291
0.5625 Remote Similarity NPC471418
0.5619 Remote Similarity NPC292758
0.5619 Remote Similarity NPC65855
0.5612 Remote Similarity NPC474164
0.5606 Remote Similarity NPC252978
0.56 Remote Similarity NPC385
0.56 Remote Similarity NPC193593
0.56 Remote Similarity NPC290106
0.56 Remote Similarity NPC143809
0.56 Remote Similarity NPC76726

  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 NPC23721 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
0.6351 Remote Similarity NPD3210 Clinical (unspecified phase)
0.6301 Remote Similarity NPD393 Approved
0.6164 Remote Similarity NPD9455 Approved
0.6 Remote Similarity NPD6949 Clinical (unspecified phase)
0.5859 Remote Similarity NPD855 Approved
0.5859 Remote Similarity NPD854 Approved
0.5844 Remote Similarity NPD9440 Discontinued
0.5802 Remote Similarity NPD3212 Clinical (unspecified phase)
0.57 Remote Similarity NPD4719 Phase 2
0.5696 Remote Similarity NPD616 Clinical (unspecified phase)
0.5636 Remote Similarity NPD7522 Discontinued
0.5625 Remote Similarity NPD9443 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