Structure

Physi-Chem Properties

Molecular Weight:  389.22
Volume:  393.324
LogP:  3.395
LogD:  3.22
LogS:  -3.875
# Rotatable Bonds:  2
TPSA:  65.07
# H-Bond Aceptor:  6
# H-Bond Donor:  0
# Rings:  5
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.677
Synthetic Accessibility Score:  5.621
Fsp3:  0.818
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.765
MDCK Permeability:  4.8584919568384066e-05
Pgp-inhibitor:  0.863
Pgp-substrate:  0.004
Human Intestinal Absorption (HIA):  0.023
20% Bioavailability (F20%):  0.876
30% Bioavailability (F30%):  0.959

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.255
Plasma Protein Binding (PPB):  54.385581970214844%
Volume Distribution (VD):  2.392
Pgp-substrate:  48.47126770019531%

ADMET: Metabolism

CYP1A2-inhibitor:  0.044
CYP1A2-substrate:  0.105
CYP2C19-inhibitor:  0.141
CYP2C19-substrate:  0.774
CYP2C9-inhibitor:  0.23
CYP2C9-substrate:  0.063
CYP2D6-inhibitor:  0.436
CYP2D6-substrate:  0.678
CYP3A4-inhibitor:  0.885
CYP3A4-substrate:  0.842

ADMET: Excretion

Clearance (CL):  10.318
Half-life (T1/2):  0.213

ADMET: Toxicity

hERG Blockers:  0.702
Human Hepatotoxicity (H-HT):  0.833
Drug-inuced Liver Injury (DILI):  0.447
AMES Toxicity:  0.059
Rat Oral Acute Toxicity:  0.554
Maximum Recommended Daily Dose:  0.21
Skin Sensitization:  0.955
Carcinogencity:  0.385
Eye Corrosion:  0.005
Eye Irritation:  0.025
Respiratory Toxicity:  0.925

Download Data

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

  Natural Product: NPC174463

Natural Product ID:  NPC174463
Common Name*:   Stemoninine
IUPAC Name:   n.a.
Synonyms:   stemoninine
Standard InCHIKey:  UINUUSQOLRQGNF-KLDYRVGWSA-N
Standard InCHI:  InChI=1S/C22H31NO5/c1-4-14-19-16-8-7-15(18-10-12(2)20(24)26-18)23(16)9-5-6-17(19)27-22(14)11-13(3)21(25)28-22/h11-12,14-19H,4-10H2,1-3H3/t12-,14-,15-,16-,17+,18-,19+,22-/m0/s1
SMILES:  CC[C@H]1[C@H]2[C@H](O[C@@]31C=C(C(=O)O3)C)CCCN1[C@H]2CC[C@H]1[C@@H]1C[C@@H](C(=O)O1)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL482474
PubChem CID:   15983991
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000279] Alkaloids and derivatives
      • [CHEMONTID:0003427] Stemona alkaloids
        • [CHEMONTID:0003914] Stemoamide-type alkaloids
          • [CHEMONTID:0003429] Stichoneurine-type alkaloids

*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
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. n.a. n.a. PMID[15679323]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota roots n.a. n.a. PMID[16643052]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota Roots; Stems; Tubers n.a. n.a. PMID[16872143]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota stems and leaves n.a. n.a. PMID[18163592]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota roots n.a. n.a. PMID[18452334]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. rhizome n.a. PMID[21902195]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. tuberous root n.a. PMID[21902195]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCM_Taiwan]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO19620 Stemona tuberosa Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO28230 Stemona japonica Species Stemonaceae 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
NPT938 Organism Cavia porcellus Cavia porcellus ID50 = 0.197 umol.kg-1 PMID[475340]
NPT938 Organism Cavia porcellus Cavia porcellus Inhibition = 90.0 % PMID[475340]
NPT938 Organism Cavia porcellus Cavia porcellus Activity = 70.0 % PMID[475340]
NPT938 Organism Cavia porcellus Cavia porcellus Inhibition = 10.0 % PMID[475340]

☑ 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 NPC174463 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
0.9123 High Similarity NPC230849
0.8595 High Similarity NPC173173
0.8584 High Similarity NPC58281
0.8319 Intermediate Similarity NPC11379
0.8306 Intermediate Similarity NPC307165
0.8175 Intermediate Similarity NPC133089
0.7903 Intermediate Similarity NPC469999
0.7759 Intermediate Similarity NPC271562
0.7597 Intermediate Similarity NPC215507
0.7583 Intermediate Similarity NPC43648
0.7559 Intermediate Similarity NPC329401
0.7559 Intermediate Similarity NPC477987
0.75 Intermediate Similarity NPC138534
0.75 Intermediate Similarity NPC477986
0.7344 Intermediate Similarity NPC471087
0.7344 Intermediate Similarity NPC326386
0.7344 Intermediate Similarity NPC477985
0.7339 Intermediate Similarity NPC65045
0.7339 Intermediate Similarity NPC469997
0.7328 Intermediate Similarity NPC477988
0.7281 Intermediate Similarity NPC471843
0.7266 Intermediate Similarity NPC111162
0.7266 Intermediate Similarity NPC293550
0.7266 Intermediate Similarity NPC323168
0.7266 Intermediate Similarity NPC477990
0.7266 Intermediate Similarity NPC477989
0.7193 Intermediate Similarity NPC150041
0.7176 Intermediate Similarity NPC471086
0.7143 Intermediate Similarity NPC235625
0.7109 Intermediate Similarity NPC470000
0.7083 Intermediate Similarity NPC93179
0.7069 Intermediate Similarity NPC476344
0.7059 Intermediate Similarity NPC265094
0.7 Intermediate Similarity NPC44514
0.6833 Remote Similarity NPC194750
0.6833 Remote Similarity NPC287638
0.6833 Remote Similarity NPC233274
0.6825 Remote Similarity NPC130124
0.6825 Remote Similarity NPC193471
0.6803 Remote Similarity NPC471844
0.6759 Remote Similarity NPC216090
0.6642 Remote Similarity NPC120335
0.6637 Remote Similarity NPC469860
0.6637 Remote Similarity NPC130436
0.6637 Remote Similarity NPC469861
0.6615 Remote Similarity NPC106791
0.6615 Remote Similarity NPC201889
0.6615 Remote Similarity NPC284656
0.6591 Remote Similarity NPC23963
0.6581 Remote Similarity NPC469998
0.6535 Remote Similarity NPC168758
0.6535 Remote Similarity NPC316984
0.6535 Remote Similarity NPC47857
0.6535 Remote Similarity NPC30911
0.6535 Remote Similarity NPC181510
0.6519 Remote Similarity NPC309525
0.6484 Remote Similarity NPC469466
0.6475 Remote Similarity NPC188785
0.6471 Remote Similarity NPC476951
0.6462 Remote Similarity NPC39041
0.6462 Remote Similarity NPC471846
0.6462 Remote Similarity NPC202722
0.6462 Remote Similarity NPC471845
0.6462 Remote Similarity NPC241294
0.6452 Remote Similarity NPC64168
0.6439 Remote Similarity NPC471261
0.6423 Remote Similarity NPC473289
0.6397 Remote Similarity NPC474371
0.6377 Remote Similarity NPC470539
0.6371 Remote Similarity NPC6271
0.6371 Remote Similarity NPC279833
0.6371 Remote Similarity NPC80439
0.6371 Remote Similarity NPC173690
0.6364 Remote Similarity NPC476952
0.6364 Remote Similarity NPC128276
0.6348 Remote Similarity NPC107787
0.6336 Remote Similarity NPC470538
0.633 Remote Similarity NPC123360
0.632 Remote Similarity NPC75523
0.632 Remote Similarity NPC133420
0.6299 Remote Similarity NPC470535
0.6283 Remote Similarity NPC173609
0.6273 Remote Similarity NPC57744
0.6271 Remote Similarity NPC159568
0.6269 Remote Similarity NPC88190
0.6268 Remote Similarity NPC471256
0.6261 Remote Similarity NPC78089
0.626 Remote Similarity NPC474984
0.625 Remote Similarity NPC470536
0.624 Remote Similarity NPC469895
0.6231 Remote Similarity NPC474995
0.6228 Remote Similarity NPC475947
0.6221 Remote Similarity NPC192306
0.6218 Remote Similarity NPC110875
0.6218 Remote Similarity NPC118844
0.6218 Remote Similarity NPC299808
0.6218 Remote Similarity NPC72183
0.621 Remote Similarity NPC474348
0.6202 Remote Similarity NPC470527
0.6202 Remote Similarity NPC470529
0.6202 Remote Similarity NPC470528
0.6202 Remote Similarity NPC470533
0.6202 Remote Similarity NPC470530
0.6202 Remote Similarity NPC470531
0.6202 Remote Similarity NPC470532
0.6195 Remote Similarity NPC301477
0.6195 Remote Similarity NPC281949
0.6195 Remote Similarity NPC25684
0.6195 Remote Similarity NPC471325
0.6187 Remote Similarity NPC478136
0.6174 Remote Similarity NPC115786
0.6169 Remote Similarity NPC475342
0.6161 Remote Similarity NPC178277
0.6154 Remote Similarity NPC147238
0.6147 Remote Similarity NPC476355
0.6134 Remote Similarity NPC80875
0.6131 Remote Similarity NPC318445
0.6131 Remote Similarity NPC316133
0.6126 Remote Similarity NPC476794
0.6126 Remote Similarity NPC470240
0.6116 Remote Similarity NPC474338
0.6107 Remote Similarity NPC276995
0.6107 Remote Similarity NPC76660
0.6107 Remote Similarity NPC1111
0.6107 Remote Similarity NPC261750
0.6107 Remote Similarity NPC60432
0.6102 Remote Similarity NPC226863
0.6098 Remote Similarity NPC150967
0.6098 Remote Similarity NPC241426
0.609 Remote Similarity NPC30196
0.609 Remote Similarity NPC288629
0.6083 Remote Similarity NPC284185
0.6077 Remote Similarity NPC127578
0.6077 Remote Similarity NPC469603
0.6068 Remote Similarity NPC284902
0.6068 Remote Similarity NPC64153
0.6063 Remote Similarity NPC477001
0.6063 Remote Similarity NPC477000
0.6061 Remote Similarity NPC469597
0.6056 Remote Similarity NPC316401
0.6054 Remote Similarity NPC281104
0.6053 Remote Similarity NPC141810
0.6053 Remote Similarity NPC42470
0.6047 Remote Similarity NPC474099
0.6047 Remote Similarity NPC15413
0.6045 Remote Similarity NPC6531
0.6045 Remote Similarity NPC147707
0.6033 Remote Similarity NPC473520
0.6031 Remote Similarity NPC470534
0.6029 Remote Similarity NPC139867
0.6018 Remote Similarity NPC182550
0.6018 Remote Similarity NPC270126
0.6017 Remote Similarity NPC475703
0.6 Remote Similarity NPC117746
0.6 Remote Similarity NPC82129
0.6 Remote Similarity NPC47230
0.6 Remote Similarity NPC15499
0.6 Remote Similarity NPC253144
0.6 Remote Similarity NPC35556
0.6 Remote Similarity NPC140287
0.6 Remote Similarity NPC469402
0.6 Remote Similarity NPC9714
0.6 Remote Similarity NPC17143
0.6 Remote Similarity NPC259599
0.6 Remote Similarity NPC294434
0.6 Remote Similarity NPC312042
0.5985 Remote Similarity NPC470277
0.5985 Remote Similarity NPC314550
0.5984 Remote Similarity NPC477131
0.5984 Remote Similarity NPC199831
0.5984 Remote Similarity NPC474827
0.5984 Remote Similarity NPC474828
0.5984 Remote Similarity NPC476267
0.5984 Remote Similarity NPC68001
0.5983 Remote Similarity NPC215364
0.5982 Remote Similarity NPC187568
0.5982 Remote Similarity NPC476028
0.5982 Remote Similarity NPC65603
0.5982 Remote Similarity NPC97516
0.5982 Remote Similarity NPC41780
0.5982 Remote Similarity NPC171204
0.5982 Remote Similarity NPC141789
0.5969 Remote Similarity NPC250187
0.5965 Remote Similarity NPC69271
0.5965 Remote Similarity NPC281132
0.5965 Remote Similarity NPC302426
0.5965 Remote Similarity NPC74673
0.5965 Remote Similarity NPC276356
0.5963 Remote Similarity NPC163003
0.595 Remote Similarity NPC74103
0.595 Remote Similarity NPC150978
0.595 Remote Similarity NPC70595
0.595 Remote Similarity NPC65513
0.595 Remote Similarity NPC123177
0.5948 Remote Similarity NPC39588
0.5948 Remote Similarity NPC318468
0.5946 Remote Similarity NPC226669
0.5946 Remote Similarity NPC193351
0.5946 Remote Similarity NPC138408
0.5944 Remote Similarity NPC315011

  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 NPC174463 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
0.6535 Remote Similarity NPD2204 Approved
0.6316 Remote Similarity NPD2132 Phase 3
0.624 Remote Similarity NPD2258 Approved
0.624 Remote Similarity NPD2259 Approved
0.6148 Remote Similarity NPD5349 Clinical (unspecified phase)
0.6131 Remote Similarity NPD7642 Approved
0.6119 Remote Similarity NPD7641 Discontinued
0.6071 Remote Similarity NPD8336 Approved
0.6071 Remote Similarity NPD8337 Approved
0.6061 Remote Similarity NPD1376 Discontinued
0.6054 Remote Similarity NPD2569 Approved
0.6054 Remote Similarity NPD2567 Approved
0.6029 Remote Similarity NPD1689 Approved
0.5944 Remote Similarity NPD2101 Approved
0.5929 Remote Similarity NPD8451 Approved
0.5903 Remote Similarity NPD8338 Approved
0.5891 Remote Similarity NPD4211 Phase 1
0.5887 Remote Similarity NPD8448 Approved
0.5874 Remote Similarity NPD8390 Approved
0.5874 Remote Similarity NPD8392 Approved
0.5874 Remote Similarity NPD8391 Approved
0.5809 Remote Similarity NPD961 Discontinued
0.5786 Remote Similarity NPD7122 Discontinued
0.5772 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5755 Remote Similarity NPD8267 Approved
0.5755 Remote Similarity NPD8268 Approved
0.5755 Remote Similarity NPD8266 Approved
0.5755 Remote Similarity NPD8269 Approved
0.5745 Remote Similarity NPD8340 Approved
0.5745 Remote Similarity NPD8342 Approved
0.5745 Remote Similarity NPD8341 Approved
0.5745 Remote Similarity NPD8299 Approved
0.5726 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8415 Approved
0.5695 Remote Similarity NPD6077 Discontinued
0.5693 Remote Similarity NPD8137 Clinical (unspecified phase)
0.568 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5676 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5656 Remote Similarity NPD1695 Approved
0.5612 Remote Similarity NPD2116 Approved
0.5612 Remote Similarity NPD2115 Approved
0.5612 Remote Similarity NPD2117 Pre-registration
0.5603 Remote Similarity NPD8080 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