Structure

Physi-Chem Properties

Molecular Weight:  950.19
Volume:  890.985
LogP:  4.45
LogD:  1.352
LogS:  -6.796
# Rotatable Bonds:  5
TPSA:  372.87
# H-Bond Aceptor:  21
# H-Bond Donor:  12
# Rings:  9
# Heavy Atoms:  21

MedChem Properties

QED Drug-Likeness Score:  0.086
Synthetic Accessibility Score:  5.824
Fsp3:  0.25
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  1

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.458
MDCK Permeability:  5.208240509091411e-06
Pgp-inhibitor:  0.859
Pgp-substrate:  0.59
Human Intestinal Absorption (HIA):  0.994
20% Bioavailability (F20%):  0.229
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.0
Plasma Protein Binding (PPB):  79.8197250366211%
Volume Distribution (VD):  0.316
Pgp-substrate:  6.9700093269348145%

ADMET: Metabolism

CYP1A2-inhibitor:  0.166
CYP1A2-substrate:  0.783
CYP2C19-inhibitor:  0.01
CYP2C19-substrate:  0.046
CYP2C9-inhibitor:  0.165
CYP2C9-substrate:  0.039
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.096
CYP3A4-inhibitor:  0.025
CYP3A4-substrate:  0.03

ADMET: Excretion

Clearance (CL):  2.196
Half-life (T1/2):  0.007

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.039
Drug-inuced Liver Injury (DILI):  0.988
AMES Toxicity:  0.155
Rat Oral Acute Toxicity:  0.002
Maximum Recommended Daily Dose:  0.06
Skin Sensitization:  0.063
Carcinogencity:  0.001
Eye Corrosion:  0.003
Eye Irritation:  0.128
Respiratory Toxicity:  0.005

Download Data

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

  Natural Product: NPC477990

Natural Product ID:  NPC477990
Common Name*:   (3'R/S)-hydroxystemofoline
IUPAC Name:   (5Z)-5-[(1S,4S,5R,6S,8S,9S,13S)-9-(3-hydroxybutyl)-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)-Hydroxystemofoline
Standard InCHIKey:  CNEADBPJIPHAPD-CQMGMYCESA-N
Standard InCHI:  InChI=1S/C22H29NO6/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/h10-11,13-16,24H,5-9H2,1-4H3/b19-18-/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)CCC(C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   n.a.
PubChem CID:   70686653
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 = 2.5 10'-2nmol 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 NPC477990 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 NPC111162
1.0 High Similarity NPC293550
1.0 High Similarity NPC477989
1.0 High Similarity NPC323168
0.9646 High Similarity NPC138534
0.9646 High Similarity NPC477986
0.9569 High Similarity NPC471087
0.9569 High Similarity NPC477985
0.9569 High Similarity NPC326386
0.9333 High Similarity NPC477988
0.9328 High Similarity NPC471086
0.916 High Similarity NPC477987
0.916 High Similarity NPC329401
0.8803 High Similarity NPC65045
0.8512 High Similarity NPC470000
0.8462 Intermediate Similarity NPC43648
0.84 Intermediate Similarity NPC173173
0.8182 Intermediate Similarity NPC469997
0.784 Intermediate Similarity NPC11379
0.7734 Intermediate Similarity NPC469999
0.7402 Intermediate Similarity NPC235625
0.7287 Intermediate Similarity NPC230849
0.7266 Intermediate Similarity NPC174463
0.6884 Remote Similarity NPC120335
0.6829 Remote Similarity NPC473289
0.6822 Remote Similarity NPC130124
0.6822 Remote Similarity NPC193471
0.6742 Remote Similarity NPC201889
0.6742 Remote Similarity NPC106791
0.6691 Remote Similarity NPC215507
0.6667 Remote Similarity NPC58281
0.6617 Remote Similarity NPC284656
0.6615 Remote Similarity NPC474995
0.6614 Remote Similarity NPC271562
0.6596 Remote Similarity NPC133089
0.6593 Remote Similarity NPC23963
0.6538 Remote Similarity NPC168758
0.6538 Remote Similarity NPC181510
0.6538 Remote Similarity NPC47857
0.6535 Remote Similarity NPC93179
0.6515 Remote Similarity NPC474984
0.6457 Remote Similarity NPC44514
0.6457 Remote Similarity NPC64168
0.6439 Remote Similarity NPC475988
0.6412 Remote Similarity NPC30911
0.6412 Remote Similarity NPC316984
0.6389 Remote Similarity NPC471256
0.6378 Remote Similarity NPC173690
0.6378 Remote Similarity NPC6271
0.6378 Remote Similarity NPC279833
0.6378 Remote Similarity NPC80439
0.6357 Remote Similarity NPC476951
0.6357 Remote Similarity NPC314282
0.6343 Remote Similarity NPC30196
0.6338 Remote Similarity NPC307165
0.6311 Remote Similarity NPC471483
0.6308 Remote Similarity NPC471636
0.6308 Remote Similarity NPC287572
0.6296 Remote Similarity NPC6531
0.629 Remote Similarity NPC473333
0.6286 Remote Similarity NPC474371
0.6279 Remote Similarity NPC471844
0.6259 Remote Similarity NPC318445
0.6259 Remote Similarity NPC316133
0.6241 Remote Similarity NPC1111
0.6241 Remote Similarity NPC261750
0.6241 Remote Similarity NPC279383
0.6241 Remote Similarity NPC60432
0.624 Remote Similarity NPC2666
0.6231 Remote Similarity NPC250187
0.6214 Remote Similarity NPC313342
0.6214 Remote Similarity NPC314451
0.6214 Remote Similarity NPC314512
0.6214 Remote Similarity NPC313333
0.621 Remote Similarity NPC471492
0.6202 Remote Similarity NPC75523
0.6202 Remote Similarity NPC469604
0.6183 Remote Similarity NPC476034
0.6183 Remote Similarity NPC474969
0.6181 Remote Similarity NPC316401
0.617 Remote Similarity NPC309525
0.6165 Remote Similarity NPC29501
0.6154 Remote Similarity NPC135216
0.6154 Remote Similarity NPC101106
0.6148 Remote Similarity NPC471184
0.6143 Remote Similarity NPC314629
0.6136 Remote Similarity NPC474891
0.6124 Remote Similarity NPC265094
0.6119 Remote Similarity NPC268327
0.6119 Remote Similarity NPC469466
0.6119 Remote Similarity NPC295444
0.6119 Remote Similarity NPC273215
0.6111 Remote Similarity NPC471490
0.6111 Remote Similarity NPC476344
0.6103 Remote Similarity NPC477554
0.6098 Remote Similarity NPC470520
0.6098 Remote Similarity NPC118844
0.6098 Remote Similarity NPC72183
0.6098 Remote Similarity NPC299808
0.6098 Remote Similarity NPC110875
0.609 Remote Similarity NPC127578
0.608 Remote Similarity NPC150041
0.6077 Remote Similarity NPC133420
0.6077 Remote Similarity NPC477000
0.6077 Remote Similarity NPC477001
0.6063 Remote Similarity NPC203627
0.6058 Remote Similarity NPC477553
0.6047 Remote Similarity NPC474244
0.6045 Remote Similarity NPC470534
0.6042 Remote Similarity NPC316205
0.6042 Remote Similarity NPC470539
0.6042 Remote Similarity NPC315387
0.6033 Remote Similarity NPC52533
0.6032 Remote Similarity NPC173329
0.6032 Remote Similarity NPC471843
0.6032 Remote Similarity NPC288350
0.6031 Remote Similarity NPC82251
0.6031 Remote Similarity NPC239961
0.6029 Remote Similarity NPC106446
0.6028 Remote Similarity NPC471255
0.6016 Remote Similarity NPC3436
0.6014 Remote Similarity NPC476952
0.6014 Remote Similarity NPC477555
0.6014 Remote Similarity NPC297058
0.6 Remote Similarity NPC476504
0.6 Remote Similarity NPC470521
0.6 Remote Similarity NPC314550
0.5987 Remote Similarity NPC71866
0.5986 Remote Similarity NPC120420
0.5984 Remote Similarity NPC52820
0.5973 Remote Similarity NPC45813
0.597 Remote Similarity NPC470532
0.597 Remote Similarity NPC470529
0.597 Remote Similarity NPC122926
0.597 Remote Similarity NPC470528
0.597 Remote Similarity NPC113012
0.597 Remote Similarity NPC470530
0.597 Remote Similarity NPC470531
0.597 Remote Similarity NPC470527
0.597 Remote Similarity NPC470533
0.597 Remote Similarity NPC469603
0.5969 Remote Similarity NPC188785
0.5969 Remote Similarity NPC198992
0.5954 Remote Similarity NPC474917
0.595 Remote Similarity NPC469861
0.595 Remote Similarity NPC130436
0.595 Remote Similarity NPC469860
0.5946 Remote Similarity NPC99864
0.594 Remote Similarity NPC475960
0.5935 Remote Similarity NPC225283
0.5923 Remote Similarity NPC121423
0.592 Remote Similarity NPC59646
0.592 Remote Similarity NPC469998
0.5915 Remote Similarity NPC186339
0.5915 Remote Similarity NPC315783
0.5909 Remote Similarity NPC475918
0.5909 Remote Similarity NPC85670
0.5899 Remote Similarity NPC476956
0.5896 Remote Similarity NPC133625
0.589 Remote Similarity NPC478139
0.5882 Remote Similarity NPC276995
0.5882 Remote Similarity NPC76660
0.5878 Remote Similarity NPC475987
0.5878 Remote Similarity NPC313348
0.5875 Remote Similarity NPC475342
0.5874 Remote Similarity NPC476503
0.5873 Remote Similarity NPC256368
0.5867 Remote Similarity NPC230889
0.5865 Remote Similarity NPC475074
0.5862 Remote Similarity NPC477793
0.5862 Remote Similarity NPC329919
0.5857 Remote Similarity NPC313802
0.5857 Remote Similarity NPC477515
0.5857 Remote Similarity NPC471261
0.5857 Remote Similarity NPC67917
0.5857 Remote Similarity NPC314268
0.5846 Remote Similarity NPC474873
0.5846 Remote Similarity NPC219038
0.5845 Remote Similarity NPC287236
0.584 Remote Similarity NPC32494
0.584 Remote Similarity NPC175842
0.5833 Remote Similarity NPC471263
0.5833 Remote Similarity NPC205176
0.5821 Remote Similarity NPC474099
0.582 Remote Similarity NPC311163
0.5814 Remote Similarity NPC270813
0.5814 Remote Similarity NPC187268
0.5802 Remote Similarity NPC471599
0.5794 Remote Similarity NPC472195
0.5794 Remote Similarity NPC189651
0.5794 Remote Similarity NPC238090
0.5794 Remote Similarity NPC472196
0.5794 Remote Similarity NPC475098
0.5794 Remote Similarity NPC472640
0.5794 Remote Similarity NPC156553
0.5794 Remote Similarity NPC472641
0.5793 Remote Similarity NPC470537
0.5793 Remote Similarity NPC280903
0.5786 Remote Similarity NPC156336
0.5786 Remote Similarity NPC200412

  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 NPC477990 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
0.6667 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6544 Remote Similarity NPD8080 Discontinued
0.6471 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6412 Remote Similarity NPD2204 Approved
0.6403 Remote Similarity NPD8451 Approved
0.637 Remote Similarity NPD7641 Discontinued
0.6357 Remote Similarity NPD8448 Approved
0.6338 Remote Similarity NPD8390 Approved
0.6338 Remote Similarity NPD8391 Approved
0.6338 Remote Similarity NPD8392 Approved
0.6259 Remote Similarity NPD7642 Approved
0.6214 Remote Similarity NPD8342 Approved
0.6214 Remote Similarity NPD8340 Approved
0.6214 Remote Similarity NPD8341 Approved
0.6214 Remote Similarity NPD8299 Approved
0.6154 Remote Similarity NPD4211 Phase 1
0.6154 Remote Similarity NPD882 Phase 2
0.6154 Remote Similarity NPD883 Phase 2
0.6138 Remote Similarity NPD6845 Suspended
0.6074 Remote Similarity NPD1376 Discontinued
0.6014 Remote Similarity NPD8387 Clinical (unspecified phase)
0.6 Remote Similarity NPD8266 Approved
0.6 Remote Similarity NPD8267 Approved
0.6 Remote Similarity NPD8268 Approved
0.6 Remote Similarity NPD8269 Approved
0.5985 Remote Similarity NPD8140 Approved
0.5946 Remote Similarity NPD8415 Approved
0.5944 Remote Similarity NPD8273 Phase 1
0.5915 Remote Similarity NPD7829 Approved
0.5915 Remote Similarity NPD7830 Approved
0.5865 Remote Similarity NPD8307 Discontinued
0.5862 Remote Similarity NPD8336 Approved
0.5862 Remote Similarity NPD8337 Approved
0.5814 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5775 Remote Similarity NPD8444 Approved
0.5745 Remote Similarity NPD2495 Phase 3
0.5743 Remote Similarity NPD2101 Approved
0.5714 Remote Similarity NPD8384 Approved
0.5705 Remote Similarity NPD2613 Approved
0.5705 Remote Similarity NPD8338 Approved
0.5704 Remote Similarity NPD6686 Approved
0.5695 Remote Similarity NPD2566 Approved
0.5695 Remote Similarity NPD2574 Discontinued
0.5695 Remote Similarity NPD2570 Approved
0.5695 Remote Similarity NPD3615 Approved
0.5695 Remote Similarity NPD3616 Approved
0.5695 Remote Similarity NPD3088 Approved
0.5695 Remote Similarity NPD3614 Approved
0.5695 Remote Similarity NPD4745 Approved
0.5695 Remote Similarity NPD2573 Approved
0.5695 Remote Similarity NPD2571 Approved
0.5695 Remote Similarity NPD3089 Approved
0.5695 Remote Similarity NPD4746 Phase 3
0.5695 Remote Similarity NPD2572 Clinical (unspecified phase)
0.5695 Remote Similarity NPD3087 Approved
0.5695 Remote Similarity NPD3090 Approved
0.5639 Remote Similarity NPD8275 Approved
0.5639 Remote Similarity NPD8276 Approved
0.5639 Remote Similarity NPD1407 Approved
0.5638 Remote Similarity NPD7260 Phase 2
0.5635 Remote Similarity NPD7838 Discovery
0.5633 Remote Similarity NPD2575 Approved
0.5621 Remote Similarity NPD4685 Phase 3
0.5621 Remote Similarity NPD4686 Approved
0.5621 Remote Similarity NPD4684 Phase 3
0.562 Remote Similarity NPD8087 Discontinued
0.5616 Remote Similarity NPD3677 Clinical (unspecified phase)

  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