Structure

Physi-Chem Properties

Molecular Weight:  403.2
Volume:  393.558
LogP:  2.955
LogD:  2.081
LogS:  -4.355
# Rotatable Bonds:  5
TPSA:  84.53
# H-Bond Aceptor:  7
# H-Bond Donor:  2
# Rings:  6
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.782
Synthetic Accessibility Score:  7.165
Fsp3:  0.727
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:  -5.396
MDCK Permeability:  5.165108450455591e-05
Pgp-inhibitor:  0.033
Pgp-substrate:  0.991
Human Intestinal Absorption (HIA):  0.355
20% Bioavailability (F20%):  0.851
30% Bioavailability (F30%):  0.981

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.833
Plasma Protein Binding (PPB):  68.7237319946289%
Volume Distribution (VD):  2.604
Pgp-substrate:  29.048707962036133%

ADMET: Metabolism

CYP1A2-inhibitor:  0.194
CYP1A2-substrate:  0.354
CYP2C19-inhibitor:  0.036
CYP2C19-substrate:  0.813
CYP2C9-inhibitor:  0.266
CYP2C9-substrate:  0.073
CYP2D6-inhibitor:  0.024
CYP2D6-substrate:  0.333
CYP3A4-inhibitor:  0.291
CYP3A4-substrate:  0.841

ADMET: Excretion

Clearance (CL):  15.805
Half-life (T1/2):  0.238

ADMET: Toxicity

hERG Blockers:  0.087
Human Hepatotoxicity (H-HT):  0.937
Drug-inuced Liver Injury (DILI):  0.87
AMES Toxicity:  0.005
Rat Oral Acute Toxicity:  0.964
Maximum Recommended Daily Dose:  0.951
Skin Sensitization:  0.476
Carcinogencity:  0.706
Eye Corrosion:  0.003
Eye Irritation:  0.01
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: NPC477988

Natural Product ID:  NPC477988
Common Name*:   (3'R/S)-stemofolenol
IUPAC Name:   (5Z)-5-[(1S,4S,5R,6S,8S,9S,13S)-9-[(E)-3-hydroxybut-1-enyl]-4-methyl-2,14-dioxa-10-azapentacyclo[6.5.1.01,5.06,10.09,13]tetradecan-3-ylidene]-4-methoxy-3-methylfuran-2-one
Synonyms:   (3'R/S)-Stemofolenol
Standard InCHIKey:  JVTGLCOWKRWBGL-BOSLILLSSA-N
Standard InCHI:  InChI=1S/C22H27NO6/c1-10(24)5-7-21-14-6-8-23(21)13-9-15(21)28-22(14)16(13)11(2)18(29-22)19-17(26-4)12(3)20(25)27-19/h5,7,10-11,13-16,24H,6,8-9H2,1-4H3/b7-5+,19-18-/t10?,11-,13-,14-,15-,16+,21-,22+/m0/s1
SMILES:  C[C@H]\1[C@@H]2[C@@H]3C[C@H]4[C@]5(N3CC[C@@H]5[C@@]2(O4)O/C1=C\6/C(=C(C(=O)O6)C)OC)/C=C/C(C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   70697067
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
NPO23955 Stemona sp. Species Stemonaceae Eukaryota n.a. n.a. n.a. PMID[15679323]
NPO23955 Stemona sp. Species Stemonaceae Eukaryota roots n.a. n.a. PMID[19222234]
NPO23955 Stemona sp. Species Stemonaceae Eukaryota n.a. n.a. n.a. PMID[19222234]
NPO23955 Stemona sp. Species Stemonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]

☑ 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 = 1.25 nM PMID[19222234]
NPT204 Individual Protein Acetylcholinesterase Homo sapiens MIC = 2.5 10'-1nmol PMID[19222234]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC = 62.5 ug/ml PMID[19222234]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC >= 125 ug/ml PMID[19222234]
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC >= 125 ug/ml PMID[19222234]
NPT20 Organism Candida albicans Candida albicans MIC >= 125 ug/ml PMID[19222234]

☑ 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 NPC477988 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
0.9664 High Similarity NPC477987
0.9664 High Similarity NPC329401
0.9333 High Similarity NPC111162
0.9333 High Similarity NPC477989
0.9333 High Similarity NPC477990
0.9333 High Similarity NPC323168
0.9333 High Similarity NPC293550
0.916 High Similarity NPC477986
0.916 High Similarity NPC138534
0.9098 High Similarity NPC326386
0.9098 High Similarity NPC477985
0.9098 High Similarity NPC471087
0.9032 High Similarity NPC471086
0.8226 Intermediate Similarity NPC65045
0.8049 Intermediate Similarity NPC43648
0.8015 Intermediate Similarity NPC173173
0.7969 Intermediate Similarity NPC470000
0.7795 Intermediate Similarity NPC469997
0.7481 Intermediate Similarity NPC230849
0.7388 Intermediate Similarity NPC469999
0.7348 Intermediate Similarity NPC11379
0.7328 Intermediate Similarity NPC235625
0.7328 Intermediate Similarity NPC174463
0.7177 Intermediate Similarity NPC473289
0.7023 Intermediate Similarity NPC193471
0.7023 Intermediate Similarity NPC130124
0.695 Remote Similarity NPC120335
0.694 Remote Similarity NPC201889
0.694 Remote Similarity NPC106791
0.687 Remote Similarity NPC168758
0.687 Remote Similarity NPC47857
0.687 Remote Similarity NPC181510
0.6815 Remote Similarity NPC284656
0.6788 Remote Similarity NPC23963
0.6744 Remote Similarity NPC93179
0.6742 Remote Similarity NPC58281
0.6692 Remote Similarity NPC474995
0.6667 Remote Similarity NPC133089
0.6667 Remote Similarity NPC44514
0.6667 Remote Similarity NPC64168
0.6643 Remote Similarity NPC215507
0.6642 Remote Similarity NPC475988
0.6617 Remote Similarity NPC316984
0.6617 Remote Similarity NPC30911
0.6593 Remote Similarity NPC474984
0.6589 Remote Similarity NPC173690
0.6589 Remote Similarity NPC80439
0.6589 Remote Similarity NPC6271
0.6589 Remote Similarity NPC279833
0.6585 Remote Similarity NPC118844
0.6585 Remote Similarity NPC110875
0.6585 Remote Similarity NPC299808
0.6585 Remote Similarity NPC72183
0.6565 Remote Similarity NPC271562
0.6549 Remote Similarity NPC476951
0.6549 Remote Similarity NPC314282
0.6544 Remote Similarity NPC30196
0.6538 Remote Similarity NPC75523
0.6528 Remote Similarity NPC307165
0.6525 Remote Similarity NPC313333
0.6525 Remote Similarity NPC313342
0.6525 Remote Similarity NPC314451
0.6525 Remote Similarity NPC314512
0.6496 Remote Similarity NPC6531
0.6493 Remote Similarity NPC29501
0.6444 Remote Similarity NPC60432
0.6444 Remote Similarity NPC268327
0.6444 Remote Similarity NPC1111
0.6444 Remote Similarity NPC273215
0.6444 Remote Similarity NPC295444
0.6444 Remote Similarity NPC261750
0.6444 Remote Similarity NPC279383
0.6439 Remote Similarity NPC250187
0.6412 Remote Similarity NPC469604
0.6406 Remote Similarity NPC203627
0.6391 Remote Similarity NPC476034
0.6391 Remote Similarity NPC471636
0.6391 Remote Similarity NPC287572
0.6391 Remote Similarity NPC474969
0.6385 Remote Similarity NPC474244
0.6378 Remote Similarity NPC473333
0.637 Remote Similarity NPC316401
0.6364 Remote Similarity NPC474371
0.6351 Remote Similarity NPC471256
0.6343 Remote Similarity NPC474891
0.6338 Remote Similarity NPC314629
0.6338 Remote Similarity NPC318445
0.6338 Remote Similarity NPC316133
0.6328 Remote Similarity NPC476344
0.6328 Remote Similarity NPC52820
0.6328 Remote Similarity NPC2666
0.6324 Remote Similarity NPC314550
0.6304 Remote Similarity NPC477554
0.6296 Remote Similarity NPC122926
0.6296 Remote Similarity NPC113012
0.6288 Remote Similarity NPC133420
0.6275 Remote Similarity NPC71866
0.6259 Remote Similarity NPC477553
0.625 Remote Similarity NPC475342
0.625 Remote Similarity NPC288350
0.625 Remote Similarity NPC173329
0.6241 Remote Similarity NPC135216
0.6241 Remote Similarity NPC101106
0.6233 Remote Similarity NPC315387
0.6233 Remote Similarity NPC316205
0.6233 Remote Similarity NPC470539
0.622 Remote Similarity NPC470521
0.6214 Remote Similarity NPC477555
0.6214 Remote Similarity NPC476952
0.6204 Remote Similarity NPC469466
0.6202 Remote Similarity NPC471490
0.619 Remote Similarity NPC470520
0.6179 Remote Similarity NPC311163
0.6176 Remote Similarity NPC469603
0.6176 Remote Similarity NPC127578
0.6172 Remote Similarity NPC150041
0.6172 Remote Similarity NPC471492
0.6165 Remote Similarity NPC477000
0.6165 Remote Similarity NPC477001
0.6165 Remote Similarity NPC474917
0.6164 Remote Similarity NPC329919
0.6164 Remote Similarity NPC477793
0.6159 Remote Similarity NPC230889
0.6159 Remote Similarity NPC45813
0.6154 Remote Similarity NPC270813
0.6148 Remote Similarity NPC474099
0.6148 Remote Similarity NPC475960
0.6144 Remote Similarity NPC315210
0.6144 Remote Similarity NPC315848
0.6142 Remote Similarity NPC59646
0.6138 Remote Similarity NPC309525
0.6129 Remote Similarity NPC316138
0.6129 Remote Similarity NPC313658
0.6119 Remote Similarity NPC239961
0.6119 Remote Similarity NPC82251
0.6111 Remote Similarity NPC3436
0.6111 Remote Similarity NPC315783
0.6111 Remote Similarity NPC471255
0.6103 Remote Similarity NPC133625
0.6098 Remote Similarity NPC471494
0.6094 Remote Similarity NPC256368
0.6093 Remote Similarity NPC297058
0.609 Remote Similarity NPC199831
0.609 Remote Similarity NPC474828
0.609 Remote Similarity NPC265094
0.609 Remote Similarity NPC474827
0.609 Remote Similarity NPC68001
0.6087 Remote Similarity NPC474497
0.6084 Remote Similarity NPC469515
0.6069 Remote Similarity NPC469494
0.6065 Remote Similarity NPC309450
0.6065 Remote Similarity NPC475266
0.6065 Remote Similarity NPC247776
0.6065 Remote Similarity NPC304299
0.6065 Remote Similarity NPC475278
0.6061 Remote Similarity NPC198992
0.6061 Remote Similarity NPC188785
0.6056 Remote Similarity NPC313802
0.6056 Remote Similarity NPC314268
0.6056 Remote Similarity NPC67917
0.6056 Remote Similarity NPC477515
0.6048 Remote Similarity NPC469860
0.6048 Remote Similarity NPC130436
0.6048 Remote Similarity NPC469861
0.6032 Remote Similarity NPC225283
0.6031 Remote Similarity NPC187268
0.6026 Remote Similarity NPC99864
0.6016 Remote Similarity NPC238090
0.6016 Remote Similarity NPC472195
0.6016 Remote Similarity NPC471483
0.6016 Remote Similarity NPC472196
0.6014 Remote Similarity NPC469455
0.6 Remote Similarity NPC475918
0.6 Remote Similarity NPC175614
0.5986 Remote Similarity NPC156336
0.5986 Remote Similarity NPC200412
0.5986 Remote Similarity NPC120599
0.5985 Remote Similarity NPC26597
0.5972 Remote Similarity NPC476504
0.5971 Remote Similarity NPC275100
0.5971 Remote Similarity NPC276995
0.5971 Remote Similarity NPC76660
0.5969 Remote Similarity NPC159698
0.596 Remote Similarity NPC120420
0.5956 Remote Similarity NPC315426
0.5954 Remote Similarity NPC98112
0.5954 Remote Similarity NPC241426
0.5943 Remote Similarity NPC474470
0.5942 Remote Similarity NPC196073
0.5942 Remote Similarity NPC195435
0.594 Remote Similarity NPC20673
0.594 Remote Similarity NPC219038
0.594 Remote Similarity NPC474873
0.594 Remote Similarity NPC175531
0.5938 Remote Similarity NPC175842
0.5938 Remote Similarity NPC32494
0.5931 Remote Similarity NPC287236
0.5931 Remote Similarity NPC20035
0.5931 Remote Similarity NPC469943
0.5926 Remote Similarity NPC314050

  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 NPC477988 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
0.6617 Remote Similarity NPD2204 Approved
0.6596 Remote Similarity NPD8451 Approved
0.6569 Remote Similarity NPD7641 Discontinued
0.6549 Remote Similarity NPD8448 Approved
0.6528 Remote Similarity NPD8391 Approved
0.6528 Remote Similarity NPD8390 Approved
0.6528 Remote Similarity NPD8392 Approved
0.6525 Remote Similarity NPD8341 Approved
0.6525 Remote Similarity NPD8342 Approved
0.6525 Remote Similarity NPD8340 Approved
0.6525 Remote Similarity NPD8299 Approved
0.6377 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6338 Remote Similarity NPD7642 Approved
0.6268 Remote Similarity NPD8080 Discontinued
0.625 Remote Similarity NPD8273 Phase 1
0.6241 Remote Similarity NPD4211 Phase 1
0.6197 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6154 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6111 Remote Similarity NPD7829 Approved
0.6111 Remote Similarity NPD7830 Approved
0.6093 Remote Similarity NPD8387 Clinical (unspecified phase)
0.6026 Remote Similarity NPD8415 Approved
0.6 Remote Similarity NPD6845 Suspended
0.5972 Remote Similarity NPD8269 Approved
0.5972 Remote Similarity NPD8266 Approved
0.5972 Remote Similarity NPD8267 Approved
0.5972 Remote Similarity NPD8268 Approved
0.5972 Remote Similarity NPD8444 Approved
0.5946 Remote Similarity NPD8337 Approved
0.5946 Remote Similarity NPD8336 Approved
0.5933 Remote Similarity NPD7260 Phase 2
0.5915 Remote Similarity NPD7505 Discontinued
0.5912 Remote Similarity NPD2575 Approved
0.5894 Remote Similarity NPD8338 Approved
0.5894 Remote Similarity NPD2613 Approved
0.5882 Remote Similarity NPD2571 Approved
0.5882 Remote Similarity NPD2574 Discontinued
0.5882 Remote Similarity NPD3614 Approved
0.5882 Remote Similarity NPD2566 Approved
0.5882 Remote Similarity NPD3087 Approved
0.5882 Remote Similarity NPD3089 Approved
0.5882 Remote Similarity NPD4746 Phase 3
0.5882 Remote Similarity NPD4745 Approved
0.5882 Remote Similarity NPD2572 Clinical (unspecified phase)
0.5882 Remote Similarity NPD3616 Approved
0.5882 Remote Similarity NPD3615 Approved
0.5882 Remote Similarity NPD2573 Approved
0.5882 Remote Similarity NPD3088 Approved
0.5882 Remote Similarity NPD2570 Approved
0.5882 Remote Similarity NPD3090 Approved
0.5859 Remote Similarity NPD7838 Discovery
0.5816 Remote Similarity NPD1376 Discontinued
0.5806 Remote Similarity NPD4684 Phase 3
0.5806 Remote Similarity NPD4685 Phase 3
0.5806 Remote Similarity NPD4686 Approved
0.5767 Remote Similarity NPD8389 Clinical (unspecified phase)
0.5753 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5745 Remote Similarity NPD6430 Approved
0.5745 Remote Similarity NPD6429 Approved
0.5735 Remote Similarity NPD1407 Approved
0.5726 Remote Similarity NPD883 Phase 2
0.5726 Remote Similarity NPD882 Phase 2
0.5714 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5714 Remote Similarity NPD6421 Discontinued
0.5714 Remote Similarity NPD7623 Phase 3
0.5696 Remote Similarity NPD8384 Approved
0.5694 Remote Similarity NPD7500 Approved
0.5683 Remote Similarity NPD6686 Approved
0.5679 Remote Similarity NPD7274 Clinical (unspecified phase)
0.5667 Remote Similarity NPD8074 Phase 3
0.5658 Remote Similarity NPD6914 Discontinued
0.5639 Remote Similarity NPD5349 Clinical (unspecified phase)
0.563 Remote Similarity NPD6648 Approved
0.5621 Remote Similarity NPD3664 Approved
0.5621 Remote Similarity NPD2101 Approved
0.5621 Remote Similarity NPD3662 Phase 3
0.5621 Remote Similarity NPD3661 Approved
0.5621 Remote Similarity NPD3663 Approved
0.5617 Remote Similarity NPD7488 Clinical (unspecified phase)
0.5615 Remote Similarity NPD6698 Approved
0.5615 Remote Similarity NPD46 Approved
0.5613 Remote Similarity NPD4621 Approved
0.5613 Remote Similarity NPD4619 Approved
0.5612 Remote Similarity NPD8140 Approved
0.5603 Remote Similarity NPD6420 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