Structure

Physi-Chem Properties

Molecular Weight:  255.18
Volume:  268.318
LogP:  1.69
LogD:  1.578
LogS:  -0.933
# Rotatable Bonds:  5
TPSA:  49.77
# H-Bond Aceptor:  4
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.748
Synthetic Accessibility Score:  4.201
Fsp3:  0.929
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.673
MDCK Permeability:  0.0001119892840506509
Pgp-inhibitor:  0.019
Pgp-substrate:  0.138
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.157

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.326
Plasma Protein Binding (PPB):  15.933040618896484%
Volume Distribution (VD):  1.037
Pgp-substrate:  77.17476654052734%

ADMET: Metabolism

CYP1A2-inhibitor:  0.121
CYP1A2-substrate:  0.124
CYP2C19-inhibitor:  0.018
CYP2C19-substrate:  0.801
CYP2C9-inhibitor:  0.002
CYP2C9-substrate:  0.075
CYP2D6-inhibitor:  0.013
CYP2D6-substrate:  0.439
CYP3A4-inhibitor:  0.023
CYP3A4-substrate:  0.388

ADMET: Excretion

Clearance (CL):  16.163
Half-life (T1/2):  0.707

ADMET: Toxicity

hERG Blockers:  0.086
Human Hepatotoxicity (H-HT):  0.121
Drug-inuced Liver Injury (DILI):  0.257
AMES Toxicity:  0.037
Rat Oral Acute Toxicity:  0.419
Maximum Recommended Daily Dose:  0.02
Skin Sensitization:  0.497
Carcinogencity:  0.108
Eye Corrosion:  0.62
Eye Irritation:  0.142
Respiratory Toxicity:  0.971

Download Data

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

  Natural Product: NPC203170

Natural Product ID:  NPC203170
Common Name*:   Gelsebamine
IUPAC Name:   (3R,3aS,4R,5S,6aS)-3-(diethylaminomethyl)-4-(hydroxymethyl)-5-methyl-3,3a,4,5,6,6a-hexahydrocyclopenta[b]furan-2-one
Synonyms:   Gelsebamine
Standard InCHIKey:  GDLVNWBONOJNFR-IEECTRCBSA-N
Standard InCHI:  InChI=1S/C14H25NO3/c1-4-15(5-2)7-10-13-11(8-16)9(3)6-12(13)18-14(10)17/h9-13,16H,4-8H2,1-3H3/t9-,10-,11+,12-,13+/m0/s1
SMILES:  OC[C@@H]1[C@@H](C)C[C@H]2[C@@H]1[C@H](CN(CC)CC)C(=O)O2
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL503405
PubChem CID:   16086588
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001283] Terpene lactones

*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
NPO21995 Gelsemium elegans Species Gelsemiaceae Eukaryota n.a. n.a. n.a. PMID[16643063]
NPO21995 Gelsemium elegans Species Gelsemiaceae Eukaryota n.a. n.a. n.a. PMID[16989532]
NPO21995 Gelsemium elegans Species Gelsemiaceae Eukaryota n.a. n.a. n.a. PMID[24256496]
NPO21995 Gelsemium elegans Species Gelsemiaceae Eukaryota leaves and vine stems Xishuangbanna Tropical Botanical Garden (XTBG), Chinese Academy of Science (CAS), Mengla County, Yunnan Province, China 2009-OCT PMID[26103517]
NPO21995 Gelsemium elegans Species Gelsemiaceae Eukaryota n.a. n.a. n.a. PMID[26222693]
NPO21995 Gelsemium elegans Species Gelsemiaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO21995 Gelsemium elegans Species Gelsemiaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO21995 Gelsemium elegans Species Gelsemiaceae 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
NPT81 Cell Line A549 Homo sapiens IC50 = 634.0 nM PMID[519928]

☑ 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 NPC203170 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
0.7212 Intermediate Similarity NPC236644
0.7176 Intermediate Similarity NPC475062
0.713 Intermediate Similarity NPC469466
0.7045 Intermediate Similarity NPC215030
0.7033 Intermediate Similarity NPC216090
0.7021 Intermediate Similarity NPC277918
0.7 Intermediate Similarity NPC70996
0.6972 Remote Similarity NPC276995
0.6972 Remote Similarity NPC76660
0.697 Remote Similarity NPC469998
0.6931 Remote Similarity NPC471843
0.6887 Remote Similarity NPC471844
0.6857 Remote Similarity NPC265094
0.6813 Remote Similarity NPC214030
0.6813 Remote Similarity NPC83108
0.6782 Remote Similarity NPC98711
0.6737 Remote Similarity NPC157328
0.6737 Remote Similarity NPC111409
0.6695 Remote Similarity NPC474371
0.6667 Remote Similarity NPC477867
0.6637 Remote Similarity NPC241294
0.6637 Remote Similarity NPC471845
0.6637 Remote Similarity NPC39041
0.6637 Remote Similarity NPC471846
0.6637 Remote Similarity NPC202722
0.6632 Remote Similarity NPC212340
0.663 Remote Similarity NPC233108
0.6596 Remote Similarity NPC156658
0.6596 Remote Similarity NPC258965
0.6579 Remote Similarity NPC209734
0.6566 Remote Similarity NPC322966
0.6526 Remote Similarity NPC126248
0.6522 Remote Similarity NPC476952
0.6495 Remote Similarity NPC291310
0.6477 Remote Similarity NPC319007
0.6465 Remote Similarity NPC52533
0.6455 Remote Similarity NPC70235
0.6446 Remote Similarity NPC212106
0.6429 Remote Similarity NPC470534
0.6413 Remote Similarity NPC179922
0.6392 Remote Similarity NPC128246
0.6373 Remote Similarity NPC474065
0.6337 Remote Similarity NPC215556
0.6306 Remote Similarity NPC15413
0.6275 Remote Similarity NPC216284
0.6271 Remote Similarity NPC470594
0.6271 Remote Similarity NPC470593
0.6271 Remote Similarity NPC88190
0.6263 Remote Similarity NPC284534
0.6263 Remote Similarity NPC204105
0.6263 Remote Similarity NPC300082
0.625 Remote Similarity NPC470424
0.6239 Remote Similarity NPC215988
0.6238 Remote Similarity NPC79549
0.6238 Remote Similarity NPC470009
0.623 Remote Similarity NPC470537
0.623 Remote Similarity NPC476951
0.623 Remote Similarity NPC280903
0.6226 Remote Similarity NPC476344
0.6222 Remote Similarity NPC28526
0.6216 Remote Similarity NPC271562
0.6211 Remote Similarity NPC470014
0.62 Remote Similarity NPC470657
0.62 Remote Similarity NPC56593
0.6195 Remote Similarity NPC470528
0.6195 Remote Similarity NPC470532
0.6195 Remote Similarity NPC470531
0.6195 Remote Similarity NPC470527
0.6195 Remote Similarity NPC470530
0.6195 Remote Similarity NPC470533
0.6195 Remote Similarity NPC470529
0.619 Remote Similarity NPC150041
0.6176 Remote Similarity NPC155935
0.6176 Remote Similarity NPC200580
0.6162 Remote Similarity NPC194859
0.6162 Remote Similarity NPC224386
0.6147 Remote Similarity NPC227622
0.6139 Remote Similarity NPC31349
0.6136 Remote Similarity NPC157518
0.6132 Remote Similarity NPC160066
0.6117 Remote Similarity NPC297474
0.6117 Remote Similarity NPC312637
0.6117 Remote Similarity NPC35809
0.6117 Remote Similarity NPC54065
0.6102 Remote Similarity NPC471109
0.6091 Remote Similarity NPC97336
0.6083 Remote Similarity NPC238323
0.6083 Remote Similarity NPC476504
0.6082 Remote Similarity NPC51507
0.6078 Remote Similarity NPC178875
0.6078 Remote Similarity NPC207114
0.6078 Remote Similarity NPC217983
0.6064 Remote Similarity NPC155441
0.6061 Remote Similarity NPC320936
0.6058 Remote Similarity NPC29821
0.6058 Remote Similarity NPC63193
0.6058 Remote Similarity NPC133888
0.6058 Remote Similarity NPC35959
0.6058 Remote Similarity NPC293001
0.6058 Remote Similarity NPC57304
0.6058 Remote Similarity NPC155215
0.6058 Remote Similarity NPC171360
0.6055 Remote Similarity NPC474348
0.6053 Remote Similarity NPC473232
0.605 Remote Similarity NPC35037
0.6042 Remote Similarity NPC475616
0.604 Remote Similarity NPC187661
0.6038 Remote Similarity NPC52044
0.6038 Remote Similarity NPC163228
0.6038 Remote Similarity NPC472873
0.6034 Remote Similarity NPC28224
0.6022 Remote Similarity NPC51249
0.6022 Remote Similarity NPC474100
0.6022 Remote Similarity NPC475232
0.6022 Remote Similarity NPC473699
0.6022 Remote Similarity NPC475260
0.6022 Remote Similarity NPC473775
0.6019 Remote Similarity NPC211087
0.6019 Remote Similarity NPC253995
0.6 Remote Similarity NPC309249
0.6 Remote Similarity NPC161035
0.6 Remote Similarity NPC470539
0.6 Remote Similarity NPC258216
0.6 Remote Similarity NPC476189
0.6 Remote Similarity NPC194750
0.6 Remote Similarity NPC200237
0.6 Remote Similarity NPC470592
0.6 Remote Similarity NPC287638
0.6 Remote Similarity NPC233274
0.5981 Remote Similarity NPC142529
0.5981 Remote Similarity NPC116683
0.5981 Remote Similarity NPC126156
0.5981 Remote Similarity NPC91771
0.598 Remote Similarity NPC239938
0.598 Remote Similarity NPC270270
0.598 Remote Similarity NPC118601
0.5966 Remote Similarity NPC235625
0.5963 Remote Similarity NPC471381
0.5962 Remote Similarity NPC246173
0.5962 Remote Similarity NPC19087
0.5962 Remote Similarity NPC77756
0.5962 Remote Similarity NPC476019
0.5962 Remote Similarity NPC301969
0.5962 Remote Similarity NPC37607
0.596 Remote Similarity NPC242771
0.596 Remote Similarity NPC100366
0.596 Remote Similarity NPC164289
0.596 Remote Similarity NPC311642
0.596 Remote Similarity NPC47135
0.5943 Remote Similarity NPC470423
0.5943 Remote Similarity NPC473331
0.5941 Remote Similarity NPC473350
0.5935 Remote Similarity NPC476503
0.5934 Remote Similarity NPC82315
0.5932 Remote Similarity NPC476502
0.5926 Remote Similarity NPC261372
0.5926 Remote Similarity NPC278028
0.5926 Remote Similarity NPC58267
0.5926 Remote Similarity NPC161493
0.5926 Remote Similarity NPC471150
0.5926 Remote Similarity NPC328180
0.5926 Remote Similarity NPC263674
0.5914 Remote Similarity NPC470243
0.5905 Remote Similarity NPC184063
0.5905 Remote Similarity NPC52756
0.5905 Remote Similarity NPC475925
0.59 Remote Similarity NPC245665
0.59 Remote Similarity NPC15091
0.5895 Remote Similarity NPC217725
0.5895 Remote Similarity NPC228411
0.5888 Remote Similarity NPC213698
0.5888 Remote Similarity NPC170120
0.5888 Remote Similarity NPC67584
0.5888 Remote Similarity NPC476053
0.5888 Remote Similarity NPC37408
0.5882 Remote Similarity NPC236692
0.5882 Remote Similarity NPC309757
0.5882 Remote Similarity NPC67493
0.5877 Remote Similarity NPC470535
0.5872 Remote Similarity NPC220111
0.5868 Remote Similarity NPC11379
0.5865 Remote Similarity NPC38392
0.5859 Remote Similarity NPC191711
0.5859 Remote Similarity NPC58631
0.5859 Remote Similarity NPC475743
0.5856 Remote Similarity NPC213528
0.5856 Remote Similarity NPC244969
0.5856 Remote Similarity NPC292803
0.5854 Remote Similarity NPC473477
0.5849 Remote Similarity NPC472238
0.5849 Remote Similarity NPC475788
0.5849 Remote Similarity NPC153590
0.5849 Remote Similarity NPC472237
0.5846 Remote Similarity NPC474210
0.5843 Remote Similarity NPC314103
0.5842 Remote Similarity NPC227051
0.5833 Remote Similarity NPC193785
0.5833 Remote Similarity NPC18019
0.5833 Remote Similarity NPC213078
0.5833 Remote Similarity NPC24956

  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 NPC203170 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
0.6514 Remote Similarity NPD8140 Approved
0.6458 Remote Similarity NPD882 Phase 2
0.6458 Remote Similarity NPD883 Phase 2
0.6364 Remote Similarity NPD8307 Discontinued
0.631 Remote Similarity NPD3198 Approved
0.625 Remote Similarity NPD375 Phase 2
0.6222 Remote Similarity NPD2695 Approved
0.6222 Remote Similarity NPD2696 Approved
0.6222 Remote Similarity NPD2697 Approved
0.6222 Remote Similarity NPD2694 Approved
0.6147 Remote Similarity NPD8085 Approved
0.6147 Remote Similarity NPD8082 Approved
0.6147 Remote Similarity NPD8083 Approved
0.6147 Remote Similarity NPD8086 Approved
0.6147 Remote Similarity NPD8138 Approved
0.6147 Remote Similarity NPD8084 Approved
0.6147 Remote Similarity NPD8139 Approved
0.6091 Remote Similarity NPD8276 Approved
0.6091 Remote Similarity NPD8275 Approved
0.6053 Remote Similarity NPD8087 Discontinued
0.6042 Remote Similarity NPD4238 Approved
0.6042 Remote Similarity NPD4802 Phase 2
0.6038 Remote Similarity NPD7991 Discontinued
0.6036 Remote Similarity NPD8081 Approved
0.5982 Remote Similarity NPD8393 Approved
0.596 Remote Similarity NPD7345 Approved
0.5917 Remote Similarity NPD7519 Approved
0.5917 Remote Similarity NPD7517 Approved
0.5917 Remote Similarity NPD7518 Approved
0.5895 Remote Similarity NPD3702 Approved
0.5876 Remote Similarity NPD617 Approved
0.5868 Remote Similarity NPD8347 Approved
0.5868 Remote Similarity NPD8346 Approved
0.5868 Remote Similarity NPD8345 Approved
0.5818 Remote Similarity NPD8418 Phase 2
0.5795 Remote Similarity NPD9676 Phase 3
0.5789 Remote Similarity NPD1828 Approved
0.5789 Remote Similarity NPD1829 Clinical (unspecified phase)
0.5789 Remote Similarity NPD1827 Clinical (unspecified phase)
0.5778 Remote Similarity NPD5193 Discontinued
0.5769 Remote Similarity NPD4264 Clinical (unspecified phase)
0.5766 Remote Similarity NPD1700 Approved
0.5763 Remote Similarity NPD8298 Phase 2
0.5752 Remote Similarity NPD4057 Clinical (unspecified phase)
0.5752 Remote Similarity NPD4056 Clinical (unspecified phase)
0.5729 Remote Similarity NPD2257 Approved
0.57 Remote Similarity NPD1448 Clinical (unspecified phase)
0.5699 Remote Similarity NPD3725 Approved
0.5699 Remote Similarity NPD3726 Approved
0.569 Remote Similarity NPD8306 Approved
0.569 Remote Similarity NPD8305 Approved
0.5688 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5652 Remote Similarity NPD7646 Clinical (unspecified phase)
0.5644 Remote Similarity NPD6435 Approved
0.5641 Remote Similarity NPD6420 Discontinued
0.562 Remote Similarity NPD8137 Clinical (unspecified phase)
0.56 Remote Similarity NPD612 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