Structure

Physi-Chem Properties

Molecular Weight:  431.19
Volume:  417.008
LogP:  3.146
LogD:  2.991
LogS:  -4.049
# Rotatable Bonds:  3
TPSA:  90.6
# H-Bond Aceptor:  8
# H-Bond Donor:  1
# Rings:  6
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.731
Synthetic Accessibility Score:  6.23
Fsp3:  0.696
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.943
MDCK Permeability:  5.668716403306462e-05
Pgp-inhibitor:  0.057
Pgp-substrate:  0.529
Human Intestinal Absorption (HIA):  0.067
20% Bioavailability (F20%):  0.894
30% Bioavailability (F30%):  0.992

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.884
Plasma Protein Binding (PPB):  78.64286041259766%
Volume Distribution (VD):  2.141
Pgp-substrate:  24.4436092376709%

ADMET: Metabolism

CYP1A2-inhibitor:  0.083
CYP1A2-substrate:  0.116
CYP2C19-inhibitor:  0.04
CYP2C19-substrate:  0.744
CYP2C9-inhibitor:  0.117
CYP2C9-substrate:  0.066
CYP2D6-inhibitor:  0.032
CYP2D6-substrate:  0.298
CYP3A4-inhibitor:  0.622
CYP3A4-substrate:  0.777

ADMET: Excretion

Clearance (CL):  13.629
Half-life (T1/2):  0.201

ADMET: Toxicity

hERG Blockers:  0.036
Human Hepatotoxicity (H-HT):  0.856
Drug-inuced Liver Injury (DILI):  0.936
AMES Toxicity:  0.02
Rat Oral Acute Toxicity:  0.806
Maximum Recommended Daily Dose:  0.418
Skin Sensitization:  0.432
Carcinogencity:  0.428
Eye Corrosion:  0.003
Eye Irritation:  0.015
Respiratory Toxicity:  0.941

Download Data

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

  Natural Product: NPC173173

Natural Product ID:  NPC173173
Common Name*:   Oxyprotostemonine
IUPAC Name:   n.a.
Synonyms:   Oxyprotostemonine
Standard InCHIKey:  YPHURJCNLMUQQJ-UHKURQFNSA-N
Standard InCHI:  InChI=1S/C23H29NO7/c1-10-8-14(28-21(10)25)17-15-9-13-16-11(2)19(20-18(27-4)12(3)22(26)29-20)31-23(16,30-15)6-5-7-24(13)17/h10-11,13-17H,5-9H2,1-4H3/b20-19-/t10-,11-,13-,14-,15-,16+,17+,23+/m0/s1
SMILES:  C[C@H]1C[C@@H]([C@@H]2[C@@H]3C[C@H]4[C@H]5[C@H](C)/C(=C/6C(=C(C)C(=O)O6)OC)/O[C@@]5(CCCN24)O3)OC1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL459913
PubChem CID:   44566737
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0003305] Aminosaccharides
            • [CHEMONTID:0000282] Aminoglycosides

*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
NPO1235 Stemona curtisii Species Stemonaceae Eukaryota n.a. n.a. n.a. PMID[15104502]
NPO1235 Stemona curtisii Species Stemonaceae Eukaryota n.a. root n.a. PMID[21049906]
NPO24472 Stemona kerrii Species Stemonaceae Eukaryota n.a. root n.a. PMID[21049906]
NPO1235 Stemona curtisii Species Stemonaceae Eukaryota n.a. n.a. n.a. PMID[21049906]
NPO24472 Stemona kerrii Species Stemonaceae Eukaryota n.a. tuberous root n.a. PMID[21902195]
NPO1235 Stemona curtisii Species Stemonaceae Eukaryota n.a. rhizome n.a. PMID[21902195]
NPO24472 Stemona kerrii Species Stemonaceae Eukaryota n.a. rhizome n.a. PMID[21902195]
NPO1235 Stemona curtisii Species Stemonaceae Eukaryota n.a. tuberous root n.a. PMID[21902195]
NPO1235 Stemona curtisii Species Stemonaceae Eukaryota n.a. n.a. n.a. PMID[21902195]
NPO1235 Stemona curtisii Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO24472 Stemona kerrii Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO1235 Stemona curtisii Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24472 Stemona kerrii Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO24472 Stemona kerrii Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO1235 Stemona curtisii 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
NPT204 Individual Protein Acetylcholinesterase Homo sapiens MIC > 1000.0 ng PMID[544613]
NPT204 Individual Protein Acetylcholinesterase Homo sapiens MIC > 2.32 nM PMID[544613]
NPT4944 Organism Anopheles minimus Anopheles minimus LC50 = 4.0 ppm PMID[544612]

☑ 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 NPC173173 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
0.8934 High Similarity NPC469999
0.8678 High Similarity NPC138534
0.8678 High Similarity NPC477986
0.8644 High Similarity NPC43648
0.8607 High Similarity NPC11379
0.8607 High Similarity NPC230849
0.8595 High Similarity NPC174463
0.84 Intermediate Similarity NPC477990
0.84 Intermediate Similarity NPC293550
0.84 Intermediate Similarity NPC477989
0.84 Intermediate Similarity NPC111162
0.84 Intermediate Similarity NPC323168
0.8361 Intermediate Similarity NPC469997
0.8361 Intermediate Similarity NPC65045
0.8333 Intermediate Similarity NPC477985
0.8333 Intermediate Similarity NPC471087
0.8333 Intermediate Similarity NPC326386
0.8268 Intermediate Similarity NPC329401
0.8268 Intermediate Similarity NPC477987
0.814 Intermediate Similarity NPC471086
0.8095 Intermediate Similarity NPC470000
0.8015 Intermediate Similarity NPC477988
0.7744 Intermediate Similarity NPC215507
0.7381 Intermediate Similarity NPC58281
0.7353 Intermediate Similarity NPC307165
0.7311 Intermediate Similarity NPC471843
0.7258 Intermediate Similarity NPC471844
0.7246 Intermediate Similarity NPC133089
0.7045 Intermediate Similarity NPC235625
0.6809 Remote Similarity NPC120335
0.6797 Remote Similarity NPC271562
0.6777 Remote Similarity NPC469998
0.6643 Remote Similarity NPC476951
0.6642 Remote Similarity NPC23963
0.6617 Remote Similarity NPC130124
0.6617 Remote Similarity NPC193471
0.6614 Remote Similarity NPC287638
0.6614 Remote Similarity NPC194750
0.6614 Remote Similarity NPC233274
0.6571 Remote Similarity NPC474371
0.6549 Remote Similarity NPC470539
0.6544 Remote Similarity NPC201889
0.6544 Remote Similarity NPC106791
0.6519 Remote Similarity NPC471846
0.6519 Remote Similarity NPC202722
0.6519 Remote Similarity NPC241294
0.6519 Remote Similarity NPC471845
0.6519 Remote Similarity NPC39041
0.6515 Remote Similarity NPC470529
0.6515 Remote Similarity NPC470527
0.6515 Remote Similarity NPC470530
0.6515 Remote Similarity NPC470528
0.6515 Remote Similarity NPC470532
0.6515 Remote Similarity NPC470533
0.6515 Remote Similarity NPC470531
0.6462 Remote Similarity NPC93179
0.6434 Remote Similarity NPC265094
0.6423 Remote Similarity NPC284656
0.6408 Remote Similarity NPC314282
0.6397 Remote Similarity NPC470538
0.6385 Remote Similarity NPC133420
0.6385 Remote Similarity NPC44514
0.6345 Remote Similarity NPC315011
0.6343 Remote Similarity NPC47857
0.6343 Remote Similarity NPC316984
0.6343 Remote Similarity NPC30911
0.6343 Remote Similarity NPC168758
0.6343 Remote Similarity NPC181510
0.6312 Remote Similarity NPC318445
0.6312 Remote Similarity NPC316133
0.6304 Remote Similarity NPC476952
0.6296 Remote Similarity NPC469466
0.6294 Remote Similarity NPC280903
0.6277 Remote Similarity NPC30196
0.6268 Remote Similarity NPC314451
0.6268 Remote Similarity NPC314512
0.6268 Remote Similarity NPC313333
0.6268 Remote Similarity NPC313342
0.6239 Remote Similarity NPC216090
0.6233 Remote Similarity NPC316401
0.6232 Remote Similarity NPC6531
0.6222 Remote Similarity NPC470534
0.6216 Remote Similarity NPC471256
0.6214 Remote Similarity NPC88190
0.6197 Remote Similarity NPC314629
0.6181 Remote Similarity NPC470537
0.6176 Remote Similarity NPC261750
0.6176 Remote Similarity NPC1111
0.6172 Remote Similarity NPC476344
0.6148 Remote Similarity NPC469860
0.6148 Remote Similarity NPC130436
0.6148 Remote Similarity NPC469861
0.6142 Remote Similarity NPC150041
0.6136 Remote Similarity NPC305157
0.6136 Remote Similarity NPC307846
0.6136 Remote Similarity NPC75523
0.6133 Remote Similarity NPC45813
0.6125 Remote Similarity NPC475342
0.6119 Remote Similarity NPC470535
0.6111 Remote Similarity NPC309525
0.6107 Remote Similarity NPC473289
0.6099 Remote Similarity NPC147635
0.6099 Remote Similarity NPC163693
0.6096 Remote Similarity NPC315387
0.6096 Remote Similarity NPC316205
0.6087 Remote Similarity NPC474984
0.6074 Remote Similarity NPC470536
0.6058 Remote Similarity NPC276995
0.6058 Remote Similarity NPC60432
0.6058 Remote Similarity NPC76660
0.6058 Remote Similarity NPC474995
0.6042 Remote Similarity NPC321197
0.604 Remote Similarity NPC475987
0.604 Remote Similarity NPC313348
0.6031 Remote Similarity NPC474348
0.6015 Remote Similarity NPC64168
0.6015 Remote Similarity NPC474917
0.6014 Remote Similarity NPC287236
0.6014 Remote Similarity NPC475988
0.6011 Remote Similarity NPC141440
0.6 Remote Similarity NPC475960
0.5984 Remote Similarity NPC471483
0.5972 Remote Similarity NPC186339
0.597 Remote Similarity NPC469401
0.5969 Remote Similarity NPC172998
0.5969 Remote Similarity NPC299396
0.5969 Remote Similarity NPC301596
0.5954 Remote Similarity NPC469402
0.5952 Remote Similarity NPC80875
0.5946 Remote Similarity NPC478139
0.594 Remote Similarity NPC80439
0.594 Remote Similarity NPC6271
0.594 Remote Similarity NPC279833
0.594 Remote Similarity NPC173690
0.5935 Remote Similarity NPC71866
0.5933 Remote Similarity NPC120420
0.5926 Remote Similarity NPC250187
0.5912 Remote Similarity NPC127578
0.5912 Remote Similarity NPC469603
0.5906 Remote Similarity NPC72183
0.5906 Remote Similarity NPC118844
0.5906 Remote Similarity NPC110875
0.5906 Remote Similarity NPC299808
0.5901 Remote Similarity NPC265699
0.5896 Remote Similarity NPC87919
0.5894 Remote Similarity NPC472428
0.5894 Remote Similarity NPC99864
0.5892 Remote Similarity NPC120671
0.5892 Remote Similarity NPC226652
0.5892 Remote Similarity NPC314100
0.5892 Remote Similarity NPC72788
0.5891 Remote Similarity NPC273197
0.5891 Remote Similarity NPC167893
0.5891 Remote Similarity NPC224689
0.5891 Remote Similarity NPC234339
0.5887 Remote Similarity NPC147707
0.5882 Remote Similarity NPC287572
0.5882 Remote Similarity NPC474969
0.5882 Remote Similarity NPC476034
0.5882 Remote Similarity NPC471636
0.5878 Remote Similarity NPC279561
0.5878 Remote Similarity NPC187268
0.5874 Remote Similarity NPC139867
0.5865 Remote Similarity NPC86077
0.5864 Remote Similarity NPC475599
0.5864 Remote Similarity NPC100612
0.5864 Remote Similarity NPC113620
0.5864 Remote Similarity NPC187497
0.5864 Remote Similarity NPC174336
0.5862 Remote Similarity NPC315783
0.5855 Remote Similarity NPC82129
0.585 Remote Similarity NPC11732
0.5845 Remote Similarity NPC200412
0.5845 Remote Similarity NPC156336
0.5845 Remote Similarity NPC476956
0.5845 Remote Similarity NPC120599
0.5844 Remote Similarity NPC473955
0.5833 Remote Similarity NPC469515
0.5833 Remote Similarity NPC473219
0.5833 Remote Similarity NPC473146
0.5833 Remote Similarity NPC470761
0.5827 Remote Similarity NPC159568
0.5821 Remote Similarity NPC215988
0.5817 Remote Similarity NPC230889
0.5816 Remote Similarity NPC477554
0.5814 Remote Similarity NPC474338
0.5814 Remote Similarity NPC473316
0.5814 Remote Similarity NPC473330
0.5811 Remote Similarity NPC478136
0.5809 Remote Similarity NPC176773
0.5806 Remote Similarity NPC281104
0.5804 Remote Similarity NPC314268
0.5804 Remote Similarity NPC313802
0.5804 Remote Similarity NPC67917
0.5804 Remote Similarity NPC477515
0.5802 Remote Similarity NPC475527
0.58 Remote Similarity NPC90814
0.58 Remote Similarity NPC189393
0.58 Remote Similarity NPC139585
0.5796 Remote Similarity NPC284625

  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 NPC173173 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
0.6593 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6475 Remote Similarity NPD8080 Discontinued
0.6454 Remote Similarity NPD8451 Approved
0.6423 Remote Similarity NPD7641 Discontinued
0.6408 Remote Similarity NPD8448 Approved
0.6403 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6389 Remote Similarity NPD8391 Approved
0.6389 Remote Similarity NPD8392 Approved
0.6389 Remote Similarity NPD8390 Approved
0.6345 Remote Similarity NPD2101 Approved
0.6343 Remote Similarity NPD2204 Approved
0.6312 Remote Similarity NPD7642 Approved
0.6268 Remote Similarity NPD8299 Approved
0.6268 Remote Similarity NPD8342 Approved
0.6268 Remote Similarity NPD8340 Approved
0.6268 Remote Similarity NPD8341 Approved
0.625 Remote Similarity NPD8337 Approved
0.625 Remote Similarity NPD8336 Approved
0.619 Remote Similarity NPD6845 Suspended
0.617 Remote Similarity NPD8269 Approved
0.617 Remote Similarity NPD8267 Approved
0.617 Remote Similarity NPD8268 Approved
0.617 Remote Similarity NPD8266 Approved
0.6143 Remote Similarity NPD2132 Phase 3
0.6081 Remote Similarity NPD8338 Approved
0.6 Remote Similarity NPD8273 Phase 1
0.596 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5926 Remote Similarity NPD8140 Approved
0.5926 Remote Similarity NPD8307 Discontinued
0.5899 Remote Similarity NPD1376 Discontinued
0.5894 Remote Similarity NPD8415 Approved
0.5874 Remote Similarity NPD1689 Approved
0.5862 Remote Similarity NPD7829 Approved
0.5862 Remote Similarity NPD7830 Approved
0.5806 Remote Similarity NPD2567 Approved
0.5806 Remote Similarity NPD2569 Approved
0.5784 Remote Similarity NPD4420 Approved
0.5769 Remote Similarity NPD7296 Approved
0.5745 Remote Similarity NPD5006 Approved
0.5745 Remote Similarity NPD5005 Approved
0.5735 Remote Similarity NPD4211 Phase 1
0.5725 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5724 Remote Similarity NPD8444 Approved
0.5704 Remote Similarity NPD8276 Approved
0.5704 Remote Similarity NPD8275 Approved
0.5695 Remote Similarity NPD7260 Phase 2
0.5691 Remote Similarity NPD882 Phase 2
0.5691 Remote Similarity NPD883 Phase 2
0.5683 Remote Similarity NPD8087 Discontinued
0.5669 Remote Similarity NPD6077 Discontinued
0.5669 Remote Similarity NPD8384 Approved
0.5658 Remote Similarity NPD2613 Approved
0.5655 Remote Similarity NPD8347 Approved
0.5655 Remote Similarity NPD8345 Approved
0.5655 Remote Similarity NPD8346 Approved
0.5652 Remote Similarity NPD6686 Approved
0.5649 Remote Similarity NPD3614 Approved
0.5649 Remote Similarity NPD2571 Approved
0.5649 Remote Similarity NPD4745 Approved
0.5649 Remote Similarity NPD3089 Approved
0.5649 Remote Similarity NPD3616 Approved
0.5649 Remote Similarity NPD2566 Approved
0.5649 Remote Similarity NPD4746 Phase 3
0.5649 Remote Similarity NPD3090 Approved
0.5649 Remote Similarity NPD2572 Clinical (unspecified phase)
0.5649 Remote Similarity NPD2574 Discontinued
0.5649 Remote Similarity NPD3087 Approved
0.5649 Remote Similarity NPD3615 Approved
0.5649 Remote Similarity NPD2570 Approved
0.5649 Remote Similarity NPD3088 Approved
0.5649 Remote Similarity NPD2573 Approved
0.563 Remote Similarity NPD8084 Approved
0.563 Remote Similarity NPD8301 Approved
0.563 Remote Similarity NPD8300 Approved
0.563 Remote Similarity NPD8139 Approved
0.563 Remote Similarity NPD8085 Approved
0.563 Remote Similarity NPD8138 Approved
0.563 Remote Similarity NPD8086 Approved
0.563 Remote Similarity NPD8082 Approved
0.563 Remote Similarity NPD8083 Approved
0.562 Remote Similarity NPD8393 Approved

  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