Structure

Physi-Chem Properties

Molecular Weight:  302.05
Volume:  275.51
LogP:  0.567
LogD:  0.675
LogS:  -3.642
# Rotatable Bonds:  2
TPSA:  118.9
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.861
Synthetic Accessibility Score:  3.399
Fsp3:  0.154
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.636
MDCK Permeability:  2.1779695089207962e-05
Pgp-inhibitor:  0.012
Pgp-substrate:  0.244
Human Intestinal Absorption (HIA):  0.73
20% Bioavailability (F20%):  0.021
30% Bioavailability (F30%):  0.334

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.176
Plasma Protein Binding (PPB):  66.8595962524414%
Volume Distribution (VD):  1.236
Pgp-substrate:  47.17198944091797%

ADMET: Metabolism

CYP1A2-inhibitor:  0.934
CYP1A2-substrate:  0.459
CYP2C19-inhibitor:  0.08
CYP2C19-substrate:  0.056
CYP2C9-inhibitor:  0.391
CYP2C9-substrate:  0.069
CYP2D6-inhibitor:  0.057
CYP2D6-substrate:  0.185
CYP3A4-inhibitor:  0.223
CYP3A4-substrate:  0.121

ADMET: Excretion

Clearance (CL):  2.559
Half-life (T1/2):  0.092

ADMET: Toxicity

hERG Blockers:  0.03
Human Hepatotoxicity (H-HT):  0.53
Drug-inuced Liver Injury (DILI):  0.98
AMES Toxicity:  0.761
Rat Oral Acute Toxicity:  0.04
Maximum Recommended Daily Dose:  0.021
Skin Sensitization:  0.154
Carcinogencity:  0.77
Eye Corrosion:  0.003
Eye Irritation:  0.043
Respiratory Toxicity:  0.928

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

  Natural Product: NPC138534

Natural Product ID:  NPC138534
Common Name*:   Stemofoline
IUPAC Name:   n.a.
Synonyms:   Stemofoline
Standard InCHIKey:  DTVYAHOULQCSMS-JQANZLKUSA-N
Standard InCHI:  InChI=1S/C22H29NO5/c1-5-6-8-21-14-7-9-23(21)13-10-15(21)27-22(14)16(13)11(2)18(28-22)19-17(25-4)12(3)20(24)26-19/h11,13-16H,5-10H2,1-4H3/b19-18-/t11-,13-,14?,15+,16+,21-,22+/m0/s1
SMILES:  CCCC[C@]12C3CCN2[C@H]2C[C@H]1O[C@@]13[C@@H]2[C@H](C)/C(=C/2C(=C(C)C(=O)O2)OC)/O1
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2304257
PubChem CID:   44448167
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]
NPO20479 Stemona burkillii Species Stemonaceae Eukaryota Stems n.a. n.a. PMID[15497953]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota stems and leaves n.a. n.a. PMID[18163592]
NPO221 Stemona aphylla Species Stemonaceae Eukaryota Roots; Stems n.a. n.a. PMID[19374387]
NPO221 Stemona aphylla Species Stemonaceae Eukaryota Stems n.a. n.a. PMID[20415428]
NPO1235 Stemona curtisii Species Stemonaceae Eukaryota n.a. n.a. n.a. PMID[21049906]
NPO27067 Stemona cochinchinensis Species Stemonaceae Eukaryota n.a. root n.a. PMID[21049906]
NPO1235 Stemona curtisii Species Stemonaceae Eukaryota n.a. root n.a. PMID[21049906]
NPO221 Stemona aphylla Species Stemonaceae Eukaryota Roots Lampang Province, Thailand 2009-APR PMID[21126060]
NPO221 Stemona aphylla Species Stemonaceae Eukaryota n.a. root n.a. PMID[21126060]
NPO1235 Stemona curtisii Species Stemonaceae Eukaryota n.a. tuberous root n.a. PMID[21902195]
NPO221 Stemona aphylla Species Stemonaceae Eukaryota n.a. n.a. 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. rhizome n.a. PMID[21902195]
NPO1235 Stemona curtisii Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO27067 Stemona cochinchinensis Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO28230 Stemona japonica 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]
NPO27067 Stemona cochinchinensis Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO28230 Stemona japonica 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]
NPO28230 Stemona japonica Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TM-MC]
NPO221 Stemona aphylla 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]
NPO27067 Stemona cochinchinensis 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]
NPO20479 Stemona burkillii 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
NPT4586 Individual Protein Nicotinic acetylcholine receptor alpha1 subunit Heliothis virescens EC50 = 50.0 nM PMID[488870]
NPT204 Individual Protein Acetylcholinesterase Homo sapiens MIC = 10.0 ng PMID[488872]
NPT487 Organism Cladosporium cladosporioides Cladosporium cladosporioides EC50 > 219.0 ppm PMID[488871]
NPT140 Organism Artemia Artemia LC50 > 33.0 ppm PMID[488871]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis LC50 = 0.59 microg/dm2 PMID[488873]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis LC50 = 1.46 ppm PMID[488873]
NPT776 Organism Spodoptera littoralis Spodoptera littoralis LC50 = 2.04 ppm PMID[488873]

☑ 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 NPC138534 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
1.0 High Similarity NPC477986
0.9646 High Similarity NPC293550
0.9646 High Similarity NPC111162
0.9646 High Similarity NPC477990
0.9646 High Similarity NPC323168
0.9646 High Similarity NPC477989
0.9478 High Similarity NPC477987
0.9478 High Similarity NPC329401
0.9224 High Similarity NPC471087
0.9224 High Similarity NPC326386
0.9224 High Similarity NPC477985
0.916 High Similarity NPC477988
0.8992 High Similarity NPC471086
0.8761 High Similarity NPC43648
0.8678 High Similarity NPC173173
0.8462 Intermediate Similarity NPC469997
0.8462 Intermediate Similarity NPC65045
0.8182 Intermediate Similarity NPC470000
0.7984 Intermediate Similarity NPC469999
0.752 Intermediate Similarity NPC11379
0.752 Intermediate Similarity NPC230849
0.75 Intermediate Similarity NPC174463
0.7087 Intermediate Similarity NPC235625
0.6889 Remote Similarity NPC215507
0.688 Remote Similarity NPC58281
0.6748 Remote Similarity NPC93179
0.6667 Remote Similarity NPC44514
0.6641 Remote Similarity NPC130124
0.6641 Remote Similarity NPC193471
0.6594 Remote Similarity NPC120335
0.6522 Remote Similarity NPC307165
0.6504 Remote Similarity NPC473289
0.6439 Remote Similarity NPC284656
0.6439 Remote Similarity NPC106791
0.6439 Remote Similarity NPC201889
0.6429 Remote Similarity NPC271562
0.6429 Remote Similarity NPC133089
0.6418 Remote Similarity NPC23963
0.64 Remote Similarity NPC75523
0.6357 Remote Similarity NPC168758
0.6357 Remote Similarity NPC47857
0.6357 Remote Similarity NPC181510
0.6336 Remote Similarity NPC474984
0.6308 Remote Similarity NPC474995
0.6303 Remote Similarity NPC72183
0.6303 Remote Similarity NPC110875
0.6303 Remote Similarity NPC299808
0.6303 Remote Similarity NPC118844
0.627 Remote Similarity NPC133420
0.626 Remote Similarity NPC475988
0.6231 Remote Similarity NPC316984
0.6231 Remote Similarity NPC30911
0.623 Remote Similarity NPC471843
0.6172 Remote Similarity NPC250187
0.6154 Remote Similarity NPC469860
0.6154 Remote Similarity NPC130436
0.6154 Remote Similarity NPC470529
0.6154 Remote Similarity NPC470532
0.6154 Remote Similarity NPC470533
0.6154 Remote Similarity NPC469861
0.6154 Remote Similarity NPC470531
0.6154 Remote Similarity NPC470530
0.6154 Remote Similarity NPC470528
0.6154 Remote Similarity NPC470527
0.6142 Remote Similarity NPC64168
0.6124 Remote Similarity NPC471636
0.6124 Remote Similarity NPC287572
0.6124 Remote Similarity NPC476034
0.6124 Remote Similarity NPC474969
0.6116 Remote Similarity NPC469998
0.6111 Remote Similarity NPC471256
0.6094 Remote Similarity NPC471844
0.6071 Remote Similarity NPC476951
0.6071 Remote Similarity NPC314282
0.6063 Remote Similarity NPC6271
0.6063 Remote Similarity NPC173690
0.6063 Remote Similarity NPC279833
0.6063 Remote Similarity NPC80439
0.6045 Remote Similarity NPC30196
0.6045 Remote Similarity NPC477554
0.6016 Remote Similarity NPC469604
0.6016 Remote Similarity NPC471492
0.6 Remote Similarity NPC6531
0.6 Remote Similarity NPC270813
0.6 Remote Similarity NPC474371
0.6 Remote Similarity NPC477553
0.5984 Remote Similarity NPC471483
0.5971 Remote Similarity NPC318445
0.5971 Remote Similarity NPC316133
0.5969 Remote Similarity NPC101106
0.5969 Remote Similarity NPC135216
0.5968 Remote Similarity NPC473333
0.5956 Remote Similarity NPC477555
0.595 Remote Similarity NPC471184
0.594 Remote Similarity NPC1111
0.594 Remote Similarity NPC261750
0.594 Remote Similarity NPC279383
0.594 Remote Similarity NPC60432
0.5938 Remote Similarity NPC265094
0.5929 Remote Similarity NPC313342
0.5929 Remote Similarity NPC314512
0.5929 Remote Similarity NPC314451
0.5929 Remote Similarity NPC313333
0.5929 Remote Similarity NPC321197
0.592 Remote Similarity NPC476344
0.592 Remote Similarity NPC471490
0.592 Remote Similarity NPC2666
0.5909 Remote Similarity NPC127578
0.5903 Remote Similarity NPC316401
0.5887 Remote Similarity NPC309525
0.5887 Remote Similarity NPC150041
0.5874 Remote Similarity NPC470539
0.5868 Remote Similarity NPC64913
0.5868 Remote Similarity NPC242877
0.5865 Remote Similarity NPC470534
0.5865 Remote Similarity NPC29501
0.5859 Remote Similarity NPC474244
0.5857 Remote Similarity NPC314629
0.5833 Remote Similarity NPC474891
0.5821 Remote Similarity NPC273215
0.5821 Remote Similarity NPC268327
0.5821 Remote Similarity NPC469466
0.5821 Remote Similarity NPC295444
0.582 Remote Similarity NPC159568
0.5794 Remote Similarity NPC153559
0.5794 Remote Similarity NPC52820
0.5789 Remote Similarity NPC469603
0.5772 Remote Similarity NPC470520
0.5769 Remote Similarity NPC477001
0.5769 Remote Similarity NPC305157
0.5769 Remote Similarity NPC307846
0.5769 Remote Similarity NPC477000
0.5764 Remote Similarity NPC315387
0.5764 Remote Similarity NPC316205
0.5758 Remote Similarity NPC470535
0.5748 Remote Similarity NPC473307
0.5748 Remote Similarity NPC124181
0.5748 Remote Similarity NPC203627
0.5745 Remote Similarity NPC471255
0.5743 Remote Similarity NPC297058
0.5735 Remote Similarity NPC106446
0.5725 Remote Similarity NPC239961
0.5725 Remote Similarity NPC476952
0.5725 Remote Similarity NPC469401
0.5725 Remote Similarity NPC82251
0.5724 Remote Similarity NPC71866
0.5714 Remote Similarity NPC120420
0.5714 Remote Similarity NPC476504
0.5714 Remote Similarity NPC470536
0.5714 Remote Similarity NPC173329
0.5714 Remote Similarity NPC288350
0.5705 Remote Similarity NPC45813
0.5704 Remote Similarity NPC314550
0.5703 Remote Similarity NPC469402
0.5702 Remote Similarity NPC52533
0.5694 Remote Similarity NPC478136
0.5693 Remote Similarity NPC470538
0.5691 Remote Similarity NPC3436
0.5685 Remote Similarity NPC315011
0.568 Remote Similarity NPC470521
0.5676 Remote Similarity NPC99864
0.5672 Remote Similarity NPC113012
0.5672 Remote Similarity NPC122926
0.5669 Remote Similarity NPC241426
0.5659 Remote Similarity NPC198992
0.5659 Remote Similarity NPC188785
0.5659 Remote Similarity NPC474348
0.5659 Remote Similarity NPC219038
0.5649 Remote Similarity NPC474917
0.5649 Remote Similarity NPC205176
0.5645 Remote Similarity NPC32494
0.5645 Remote Similarity NPC175842
0.5639 Remote Similarity NPC474099
0.5639 Remote Similarity NPC475960
0.5635 Remote Similarity NPC291709
0.5635 Remote Similarity NPC241407
0.5634 Remote Similarity NPC186339
0.5634 Remote Similarity NPC315783
0.563 Remote Similarity NPC170286
0.5625 Remote Similarity NPC280903
0.5625 Remote Similarity NPC475342
0.5621 Remote Similarity NPC475845
0.5616 Remote Similarity NPC478139
0.5615 Remote Similarity NPC121423
0.5615 Remote Similarity NPC233274
0.5615 Remote Similarity NPC194750
0.5615 Remote Similarity NPC471599
0.5615 Remote Similarity NPC287638
0.5612 Remote Similarity NPC200412
0.5612 Remote Similarity NPC156336
0.5612 Remote Similarity NPC476956
0.5612 Remote Similarity NPC120599
0.561 Remote Similarity NPC225283
0.5608 Remote Similarity NPC313348
0.5608 Remote Similarity NPC475987
0.5606 Remote Similarity NPC475918
0.5606 Remote Similarity NPC85670
0.5606 Remote Similarity NPC86906
0.5603 Remote Similarity NPC469515
0.56 Remote Similarity NPC59646

  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 NPC138534 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
0.6364 Remote Similarity NPD8137 Clinical (unspecified phase)
0.625 Remote Similarity NPD8080 Discontinued
0.6231 Remote Similarity NPD2204 Approved
0.6176 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6115 Remote Similarity NPD8451 Approved
0.6074 Remote Similarity NPD7641 Discontinued
0.6071 Remote Similarity NPD8448 Approved
0.6056 Remote Similarity NPD8391 Approved
0.6056 Remote Similarity NPD8390 Approved
0.6056 Remote Similarity NPD8392 Approved
0.6028 Remote Similarity NPD8336 Approved
0.6028 Remote Similarity NPD8337 Approved
0.5972 Remote Similarity NPD6845 Suspended
0.5971 Remote Similarity NPD7642 Approved
0.5969 Remote Similarity NPD4211 Phase 1
0.5929 Remote Similarity NPD8342 Approved
0.5929 Remote Similarity NPD8340 Approved
0.5929 Remote Similarity NPD8299 Approved
0.5929 Remote Similarity NPD8341 Approved
0.5862 Remote Similarity NPD8338 Approved
0.5812 Remote Similarity NPD883 Phase 2
0.5812 Remote Similarity NPD882 Phase 2
0.5778 Remote Similarity NPD1376 Discontinued
0.5743 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5714 Remote Similarity NPD8267 Approved
0.5714 Remote Similarity NPD8268 Approved
0.5714 Remote Similarity NPD8266 Approved
0.5714 Remote Similarity NPD8269 Approved
0.5685 Remote Similarity NPD2101 Approved
0.5682 Remote Similarity NPD8140 Approved
0.5676 Remote Similarity NPD8415 Approved
0.5664 Remote Similarity NPD8273 Phase 1
0.5634 Remote Similarity NPD7829 Approved
0.5634 Remote Similarity NPD7830 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