Structure

Physi-Chem Properties

Molecular Weight:  468.21
Volume:  464.002
LogP:  2.358
LogD:  1.967
LogS:  -4.609
# Rotatable Bonds:  3
TPSA:  101.8
# H-Bond Aceptor:  7
# H-Bond Donor:  1
# Rings:  7
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.404
Synthetic Accessibility Score:  5.937
Fsp3:  0.704
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
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:  -5.032
MDCK Permeability:  2.4590106477262452e-05
Pgp-inhibitor:  0.88
Pgp-substrate:  0.612
Human Intestinal Absorption (HIA):  0.052
20% Bioavailability (F20%):  0.162
30% Bioavailability (F30%):  0.973

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.902
Plasma Protein Binding (PPB):  88.47295379638672%
Volume Distribution (VD):  2.153
Pgp-substrate:  13.077850341796875%

ADMET: Metabolism

CYP1A2-inhibitor:  0.023
CYP1A2-substrate:  0.175
CYP2C19-inhibitor:  0.022
CYP2C19-substrate:  0.35
CYP2C9-inhibitor:  0.046
CYP2C9-substrate:  0.016
CYP2D6-inhibitor:  0.017
CYP2D6-substrate:  0.135
CYP3A4-inhibitor:  0.868
CYP3A4-substrate:  0.362

ADMET: Excretion

Clearance (CL):  8.26
Half-life (T1/2):  0.646

ADMET: Toxicity

hERG Blockers:  0.105
Human Hepatotoxicity (H-HT):  0.159
Drug-inuced Liver Injury (DILI):  0.872
AMES Toxicity:  0.025
Rat Oral Acute Toxicity:  0.994
Maximum Recommended Daily Dose:  0.963
Skin Sensitization:  0.152
Carcinogencity:  0.718
Eye Corrosion:  0.01
Eye Irritation:  0.016
Respiratory Toxicity:  0.985

Download Data

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

  Natural Product: NPC470994

Natural Product ID:  NPC470994
Common Name*:   Microgrewiapine A 3-Acetate
IUPAC Name:   [(2S,3R,6S)-6-[(1E,3E,5E)-deca-1,3,5-trienyl]-1,2-dimethylpiperidin-3-yl] acetate
Synonyms:   Microgrewiapine A 3-Acetate
Standard InCHIKey:  JMQLJAPSKRBPMT-YFKNEZHJSA-N
Standard InCHI:  InChI=1S/C19H31NO2/c1-5-6-7-8-9-10-11-12-13-18-14-15-19(22-17(3)21)16(2)20(18)4/h8-13,16,18-19H,5-7,14-15H2,1-4H3/b9-8+,11-10+,13-12+/t16-,18+,19+/m0/s1
SMILES:  CCCC/C=C/C=C/C=C/[C@@H]1CC[C@H]([C@@H](N1C)C)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2334873
PubChem CID:   71578973
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[532796]
NPT409 Protein Complex Neuronal acetylcholine receptor; alpha4/beta2 Homo sapiens Inhibition = 44.1 % PMID[532796]

☑ 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 NPC470994 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
0.8194 Intermediate Similarity NPC23721
0.7895 Intermediate Similarity NPC470993
0.7895 Intermediate Similarity NPC470992
0.7532 Intermediate Similarity NPC26932
0.7108 Intermediate Similarity NPC209232
0.6795 Remote Similarity NPC474812
0.6707 Remote Similarity NPC281154
0.6667 Remote Similarity NPC474833
0.663 Remote Similarity NPC118844
0.663 Remote Similarity NPC110875
0.663 Remote Similarity NPC299808
0.663 Remote Similarity NPC72183
0.6585 Remote Similarity NPC78562
0.6585 Remote Similarity NPC473588
0.6566 Remote Similarity NPC75523
0.6562 Remote Similarity NPC270813
0.6533 Remote Similarity NPC42477
0.6531 Remote Similarity NPC473289
0.6512 Remote Similarity NPC477523
0.6506 Remote Similarity NPC34672
0.6494 Remote Similarity NPC206660
0.6486 Remote Similarity NPC319991
0.6471 Remote Similarity NPC475363
0.6471 Remote Similarity NPC473972
0.6471 Remote Similarity NPC473971
0.6437 Remote Similarity NPC477524
0.642 Remote Similarity NPC97614
0.6404 Remote Similarity NPC475975
0.64 Remote Similarity NPC477000
0.64 Remote Similarity NPC477001
0.6395 Remote Similarity NPC471768
0.6353 Remote Similarity NPC325936
0.6289 Remote Similarity NPC241426
0.6265 Remote Similarity NPC208657
0.6087 Remote Similarity NPC469860
0.6087 Remote Similarity NPC469861
0.6087 Remote Similarity NPC130436
0.6078 Remote Similarity NPC44514
0.604 Remote Similarity NPC474244
0.6019 Remote Similarity NPC93179
0.6 Remote Similarity NPC474312
0.596 Remote Similarity NPC52820
0.5955 Remote Similarity NPC476560
0.5949 Remote Similarity NPC477106
0.5941 Remote Similarity NPC188785
0.5934 Remote Similarity NPC178758
0.5934 Remote Similarity NPC196102
0.5921 Remote Similarity NPC44542
0.5915 Remote Similarity NPC207815
0.5909 Remote Similarity NPC473446
0.5909 Remote Similarity NPC473695
0.5904 Remote Similarity NPC45060
0.5904 Remote Similarity NPC280065
0.5895 Remote Similarity NPC81195
0.5872 Remote Similarity NPC474984
0.5859 Remote Similarity NPC175614
0.5833 Remote Similarity NPC53240
0.5833 Remote Similarity NPC43648
0.5833 Remote Similarity NPC474995
0.5823 Remote Similarity NPC252684
0.5823 Remote Similarity NPC47333
0.5806 Remote Similarity NPC296589
0.58 Remote Similarity NPC91036
0.5794 Remote Similarity NPC63511
0.5783 Remote Similarity NPC249713
0.5776 Remote Similarity NPC329401
0.5776 Remote Similarity NPC477987
0.5769 Remote Similarity NPC222852
0.5769 Remote Similarity NPC205176
0.5769 Remote Similarity NPC133923
0.5769 Remote Similarity NPC133420
0.5758 Remote Similarity NPC471635
0.5758 Remote Similarity NPC476261
0.5758 Remote Similarity NPC25033
0.5758 Remote Similarity NPC470382
0.5758 Remote Similarity NPC119225
0.5755 Remote Similarity NPC474099
0.5755 Remote Similarity NPC287572
0.5755 Remote Similarity NPC471636
0.5747 Remote Similarity NPC3094
0.5741 Remote Similarity NPC469455
0.5732 Remote Similarity NPC113224
0.5729 Remote Similarity NPC159369
0.5729 Remote Similarity NPC39290
0.5714 Remote Similarity NPC475930
0.5714 Remote Similarity NPC127145
0.5714 Remote Similarity NPC226982
0.5714 Remote Similarity NPC277341
0.5698 Remote Similarity NPC305223
0.5686 Remote Similarity NPC233932
0.5684 Remote Similarity NPC324506
0.5676 Remote Similarity NPC106531
0.5673 Remote Similarity NPC474828
0.5673 Remote Similarity NPC68001
0.5673 Remote Similarity NPC6271
0.5673 Remote Similarity NPC474827
0.5673 Remote Similarity NPC199831
0.5673 Remote Similarity NPC55336
0.566 Remote Similarity NPC271562
0.5658 Remote Similarity NPC474913
0.5647 Remote Similarity NPC474674
0.5641 Remote Similarity NPC385
0.5641 Remote Similarity NPC469373
0.5641 Remote Similarity NPC471421
0.5641 Remote Similarity NPC325734
0.5641 Remote Similarity NPC233364
0.5631 Remote Similarity NPC100810
0.5631 Remote Similarity NPC144714
0.5631 Remote Similarity NPC474348
0.5625 Remote Similarity NPC469997
0.5625 Remote Similarity NPC65045
0.5619 Remote Similarity NPC64168
0.5612 Remote Similarity NPC145707
0.561 Remote Similarity NPC182794
0.561 Remote Similarity NPC476655
0.561 Remote Similarity NPC322319
0.561 Remote Similarity NPC326651
0.561 Remote Similarity NPC476654
0.561 Remote Similarity NPC476657
0.561 Remote Similarity NPC325117

  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 NPC470994 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
0.6526 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6341 Remote Similarity NPD6704 Discontinued
0.5904 Remote Similarity NPD2694 Approved
0.5904 Remote Similarity NPD2697 Approved
0.5904 Remote Similarity NPD2696 Approved
0.5904 Remote Similarity NPD2695 Approved
0.5875 Remote Similarity NPD9648 Approved
0.5856 Remote Similarity NPD4574 Approved
0.5856 Remote Similarity NPD4576 Approved
0.581 Remote Similarity NPD5704 Approved
0.581 Remote Similarity NPD5705 Approved
0.581 Remote Similarity NPD5706 Approved
0.5747 Remote Similarity NPD1452 Discontinued
0.5732 Remote Similarity NPD616 Clinical (unspecified phase)
0.5652 Remote Similarity NPD882 Phase 2
0.5652 Remote Similarity NPD883 Phase 2
0.5625 Remote Similarity NPD6949 Clinical (unspecified phase)
0.5625 Remote Similarity NPD3205 Discontinued

  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