Structure

Physi-Chem Properties

Molecular Weight:  405.22
Volume:  396.195
LogP:  3.594
LogD:  3.47
LogS:  -4.206
# 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:  0.779
Synthetic Accessibility Score:  7.294
Fsp3:  0.818
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:  -5.018
MDCK Permeability:  2.558653250162024e-05
Pgp-inhibitor:  0.012
Pgp-substrate:  0.644
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.006
30% Bioavailability (F30%):  0.885

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.813
Plasma Protein Binding (PPB):  87.43846893310547%
Volume Distribution (VD):  3.159
Pgp-substrate:  12.124855995178223%

ADMET: Metabolism

CYP1A2-inhibitor:  0.022
CYP1A2-substrate:  0.419
CYP2C19-inhibitor:  0.029
CYP2C19-substrate:  0.898
CYP2C9-inhibitor:  0.28
CYP2C9-substrate:  0.073
CYP2D6-inhibitor:  0.006
CYP2D6-substrate:  0.267
CYP3A4-inhibitor:  0.475
CYP3A4-substrate:  0.812

ADMET: Excretion

Clearance (CL):  14.121
Half-life (T1/2):  0.284

ADMET: Toxicity

hERG Blockers:  0.055
Human Hepatotoxicity (H-HT):  0.967
Drug-inuced Liver Injury (DILI):  0.961
AMES Toxicity:  0.032
Rat Oral Acute Toxicity:  0.963
Maximum Recommended Daily Dose:  0.953
Skin Sensitization:  0.482
Carcinogencity:  0.825
Eye Corrosion:  0.003
Eye Irritation:  0.018
Respiratory Toxicity:  0.978

Download Data

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

  Natural Product: NPC471087

Natural Product ID:  NPC471087
Common Name*:   6Beta-Hydroxystemofoline
IUPAC Name:   n.a.
Synonyms:   6beta-hydroxystemofoline
Standard InCHIKey:  UYJQMJHUNWUKTG-YLMSMMQMSA-N
Standard InCHI:  InChI=1S/C22H31NO6/c1-5-6-7-21-14-8-12-15-10(2)17(18-16(26-4)11(3)20(25)27-18)29-22(15,28-14)19(21)13(24)9-23(12)21/h10,12-15,17-19,24H,5-9H2,1-4H3/t10-,12-,13+,14+,15+,17?,18?,19+,21-,22-/m0/s1
SMILES:  CCCC[C@@]12[C@H]3C[C@@H]4N1C[C@H]([C@H]2[C@]1(O3)[C@@H]4[C@@H](C(O1)C1OC(=O)C(=C1OC)C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2368529
PubChem CID:   73345325
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
NPO28230 Stemona japonica Species Stemonaceae Eukaryota stems and leaves n.a. n.a. PMID[18163592]
NPO28230 Stemona japonica 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]
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]
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
NPT4586 Individual Protein Nicotinic acetylcholine receptor alpha1 subunit Heliothis virescens EC50 = 157.0 nM PMID[544292]

☑ 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 NPC471087 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 NPC326386
1.0 High Similarity NPC477985
0.9744 High Similarity NPC471086
0.9569 High Similarity NPC293550
0.9569 High Similarity NPC323168
0.9569 High Similarity NPC111162
0.9569 High Similarity NPC477990
0.9569 High Similarity NPC477989
0.9224 High Similarity NPC477986
0.9224 High Similarity NPC138534
0.9098 High Similarity NPC477988
0.8926 High Similarity NPC329401
0.8926 High Similarity NPC477987
0.8417 Intermediate Similarity NPC65045
0.8333 Intermediate Similarity NPC173173
0.8145 Intermediate Similarity NPC470000
0.8083 Intermediate Similarity NPC43648
0.7823 Intermediate Similarity NPC469997
0.7638 Intermediate Similarity NPC11379
0.75 Intermediate Similarity NPC230849
0.748 Intermediate Similarity NPC235625
0.7405 Intermediate Similarity NPC469999
0.7344 Intermediate Similarity NPC174463
0.6947 Remote Similarity NPC201889
0.6947 Remote Similarity NPC106791
0.6899 Remote Similarity NPC130124
0.6899 Remote Similarity NPC193471
0.6884 Remote Similarity NPC215507
0.6791 Remote Similarity NPC23963
0.6786 Remote Similarity NPC133089
0.6746 Remote Similarity NPC93179
0.6714 Remote Similarity NPC120335
0.6692 Remote Similarity NPC474995
0.6692 Remote Similarity NPC284656
0.6667 Remote Similarity NPC44514
0.6667 Remote Similarity NPC64168
0.6641 Remote Similarity NPC475988
0.664 Remote Similarity NPC473289
0.6615 Remote Similarity NPC168758
0.6615 Remote Similarity NPC181510
0.6615 Remote Similarity NPC47857
0.6615 Remote Similarity NPC316984
0.6615 Remote Similarity NPC30911
0.6615 Remote Similarity NPC58281
0.6591 Remote Similarity NPC474984
0.6587 Remote Similarity NPC173690
0.6587 Remote Similarity NPC80439
0.6587 Remote Similarity NPC6271
0.6587 Remote Similarity NPC279833
0.6562 Remote Similarity NPC271562
0.6547 Remote Similarity NPC476951
0.6541 Remote Similarity NPC30196
0.6529 Remote Similarity NPC471483
0.6525 Remote Similarity NPC307165
0.6493 Remote Similarity NPC6531
0.6484 Remote Similarity NPC471844
0.6475 Remote Similarity NPC474371
0.6458 Remote Similarity NPC471256
0.6449 Remote Similarity NPC316133
0.6449 Remote Similarity NPC318445
0.6439 Remote Similarity NPC261750
0.6439 Remote Similarity NPC1111
0.6439 Remote Similarity NPC279383
0.6364 Remote Similarity NPC316401
0.6336 Remote Similarity NPC474891
0.6316 Remote Similarity NPC60432
0.6316 Remote Similarity NPC295444
0.6316 Remote Similarity NPC273215
0.6316 Remote Similarity NPC268327
0.6312 Remote Similarity NPC314282
0.6308 Remote Similarity NPC250187
0.626 Remote Similarity NPC476034
0.626 Remote Similarity NPC474969
0.6241 Remote Similarity NPC309525
0.624 Remote Similarity NPC473333
0.6231 Remote Similarity NPC101106
0.6231 Remote Similarity NPC135216
0.623 Remote Similarity NPC471184
0.6224 Remote Similarity NPC470539
0.6204 Remote Similarity NPC476952
0.6202 Remote Similarity NPC265094
0.6194 Remote Similarity NPC469466
0.619 Remote Similarity NPC297058
0.619 Remote Similarity NPC2666
0.6187 Remote Similarity NPC476504
0.617 Remote Similarity NPC313342
0.617 Remote Similarity NPC313333
0.617 Remote Similarity NPC314451
0.617 Remote Similarity NPC314512
0.6165 Remote Similarity NPC127578
0.616 Remote Similarity NPC471492
0.6154 Remote Similarity NPC75523
0.6154 Remote Similarity NPC474917
0.6136 Remote Similarity NPC475960
0.6136 Remote Similarity NPC471636
0.6136 Remote Similarity NPC287572
0.6119 Remote Similarity NPC29501
0.6116 Remote Similarity NPC52533
0.6111 Remote Similarity NPC471843
0.6107 Remote Similarity NPC475918
0.6107 Remote Similarity NPC239961
0.6099 Remote Similarity NPC186339
0.6099 Remote Similarity NPC471255
0.6099 Remote Similarity NPC314629
0.6084 Remote Similarity NPC470537
0.6084 Remote Similarity NPC280903
0.608 Remote Similarity NPC256368
0.6074 Remote Similarity NPC76660
0.6074 Remote Similarity NPC276995
0.6063 Remote Similarity NPC476344
0.6063 Remote Similarity NPC471490
0.6056 Remote Similarity NPC476503
0.6054 Remote Similarity NPC313348
0.6054 Remote Similarity NPC475987
0.6054 Remote Similarity NPC120420
0.6048 Remote Similarity NPC470520
0.6047 Remote Similarity NPC198992
0.6045 Remote Similarity NPC122926
0.6045 Remote Similarity NPC113012
0.604 Remote Similarity NPC45813
0.6032 Remote Similarity NPC150041
0.6031 Remote Similarity NPC477000
0.6031 Remote Similarity NPC477001
0.6028 Remote Similarity NPC469943
0.6027 Remote Similarity NPC139585
0.6027 Remote Similarity NPC315011
0.6016 Remote Similarity NPC187268
0.6014 Remote Similarity NPC99864
0.6 Remote Similarity NPC472195
0.6 Remote Similarity NPC470534
0.6 Remote Similarity NPC315387
0.6 Remote Similarity NPC472196
0.6 Remote Similarity NPC238090
0.6 Remote Similarity NPC156553
0.6 Remote Similarity NPC121423
0.6 Remote Similarity NPC316205
0.5985 Remote Similarity NPC85670
0.5984 Remote Similarity NPC98165
0.5984 Remote Similarity NPC173329
0.5984 Remote Similarity NPC288350
0.5971 Remote Similarity NPC120599
0.5971 Remote Similarity NPC156336
0.5971 Remote Similarity NPC200412
0.597 Remote Similarity NPC257853
0.5968 Remote Similarity NPC3436
0.5959 Remote Similarity NPC478139
0.5956 Remote Similarity NPC275100
0.5952 Remote Similarity NPC470521
0.5952 Remote Similarity NPC159698
0.5946 Remote Similarity NPC477072
0.5942 Remote Similarity NPC39041
0.5942 Remote Similarity NPC202722
0.5942 Remote Similarity NPC477554
0.5942 Remote Similarity NPC471845
0.5942 Remote Similarity NPC471846
0.5942 Remote Similarity NPC241294
0.594 Remote Similarity NPC176773
0.5938 Remote Similarity NPC475342
0.5929 Remote Similarity NPC471261
0.5926 Remote Similarity NPC470527
0.5926 Remote Similarity NPC470528
0.5926 Remote Similarity NPC470533
0.5926 Remote Similarity NPC470531
0.5926 Remote Similarity NPC470530
0.5926 Remote Similarity NPC470532
0.5926 Remote Similarity NPC470529
0.5923 Remote Similarity NPC474873
0.5923 Remote Similarity NPC188785
0.592 Remote Similarity NPC72183
0.592 Remote Similarity NPC110875
0.592 Remote Similarity NPC299808
0.592 Remote Similarity NPC118844
0.5915 Remote Similarity NPC20035
0.5912 Remote Similarity NPC265699
0.5912 Remote Similarity NPC475527
0.5909 Remote Similarity NPC161775
0.5909 Remote Similarity NPC469604
0.5903 Remote Similarity NPC471263
0.5902 Remote Similarity NPC311163
0.5899 Remote Similarity NPC477553
0.5896 Remote Similarity NPC70235
0.5891 Remote Similarity NPC203627
0.5887 Remote Similarity NPC88190
0.5887 Remote Similarity NPC133450
0.5887 Remote Similarity NPC225283
0.5878 Remote Similarity NPC86077
0.5878 Remote Similarity NPC474244
0.5875 Remote Similarity NPC187497
0.5875 Remote Similarity NPC174336
0.5875 Remote Similarity NPC113620
0.5875 Remote Similarity NPC100612
0.5875 Remote Similarity NPC475599
0.5874 Remote Similarity NPC315783
0.5873 Remote Similarity NPC469998
0.5873 Remote Similarity NPC59646
0.5873 Remote Similarity NPC472641
0.5873 Remote Similarity NPC472640
0.587 Remote Similarity NPC106446
0.5865 Remote Similarity NPC82251
0.5862 Remote Similarity NPC11732

  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 NPC471087 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
0.687 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6741 Remote Similarity NPD8080 Discontinued
0.6667 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6615 Remote Similarity NPD2204 Approved
0.6449 Remote Similarity NPD7642 Approved
0.6357 Remote Similarity NPD8451 Approved
0.6324 Remote Similarity NPD7641 Discontinued
0.6312 Remote Similarity NPD8448 Approved
0.6294 Remote Similarity NPD8391 Approved
0.6294 Remote Similarity NPD8390 Approved
0.6294 Remote Similarity NPD8392 Approved
0.6239 Remote Similarity NPD883 Phase 2
0.6239 Remote Similarity NPD882 Phase 2
0.6231 Remote Similarity NPD4211 Phase 1
0.6187 Remote Similarity NPD8268 Approved
0.6187 Remote Similarity NPD8269 Approved
0.6187 Remote Similarity NPD8266 Approved
0.6187 Remote Similarity NPD8267 Approved
0.617 Remote Similarity NPD8299 Approved
0.617 Remote Similarity NPD8340 Approved
0.617 Remote Similarity NPD8342 Approved
0.617 Remote Similarity NPD8341 Approved
0.6081 Remote Similarity NPD8387 Clinical (unspecified phase)
0.6061 Remote Similarity NPD8307 Discontinued
0.6061 Remote Similarity NPD8140 Approved
0.6029 Remote Similarity NPD1376 Discontinued
0.6027 Remote Similarity NPD2101 Approved
0.6014 Remote Similarity NPD8415 Approved
0.5986 Remote Similarity NPD6845 Suspended
0.5954 Remote Similarity NPD1407 Approved
0.5931 Remote Similarity NPD8337 Approved
0.5931 Remote Similarity NPD8336 Approved
0.5903 Remote Similarity NPD8273 Phase 1
0.5874 Remote Similarity NPD7829 Approved
0.5874 Remote Similarity NPD7830 Approved
0.5816 Remote Similarity NPD2132 Phase 3
0.5809 Remote Similarity NPD8087 Discontinued
0.5779 Remote Similarity NPD8384 Approved
0.5778 Remote Similarity NPD6686 Approved
0.5775 Remote Similarity NPD8347 Approved
0.5775 Remote Similarity NPD8346 Approved
0.5775 Remote Similarity NPD8345 Approved
0.5772 Remote Similarity NPD8338 Approved
0.5734 Remote Similarity NPD8444 Approved
0.5714 Remote Similarity NPD8275 Approved
0.5714 Remote Similarity NPD6698 Approved
0.5714 Remote Similarity NPD8276 Approved
0.5714 Remote Similarity NPD46 Approved
0.5704 Remote Similarity NPD2495 Phase 3
0.5667 Remote Similarity NPD2613 Approved
0.5658 Remote Similarity NPD2571 Approved
0.5658 Remote Similarity NPD2573 Approved
0.5658 Remote Similarity NPD3087 Approved
0.5658 Remote Similarity NPD3615 Approved
0.5658 Remote Similarity NPD2574 Discontinued
0.5658 Remote Similarity NPD3088 Approved
0.5658 Remote Similarity NPD2570 Approved
0.5658 Remote Similarity NPD3090 Approved
0.5658 Remote Similarity NPD3614 Approved
0.5658 Remote Similarity NPD2572 Clinical (unspecified phase)
0.5658 Remote Similarity NPD3089 Approved
0.5658 Remote Similarity NPD4745 Approved
0.5658 Remote Similarity NPD4746 Phase 3
0.5658 Remote Similarity NPD2566 Approved
0.5658 Remote Similarity NPD3616 Approved
0.5649 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5639 Remote Similarity NPD8082 Approved
0.5639 Remote Similarity NPD8085 Approved
0.5639 Remote Similarity NPD8139 Approved
0.5639 Remote Similarity NPD8084 Approved
0.5639 Remote Similarity NPD8083 Approved
0.5639 Remote Similarity NPD8086 Approved
0.5639 Remote Similarity NPD8138 Approved
0.563 Remote Similarity NPD8393 Approved
0.5615 Remote Similarity NPD3189 Approved
0.5615 Remote Similarity NPD3190 Approved
0.5615 Remote Similarity NPD3191 Approved
0.5612 Remote Similarity NPD6429 Approved
0.5612 Remote Similarity NPD6430 Approved
0.561 Remote Similarity NPD8414 Discontinued
0.5603 Remote Similarity NPD4830 Approved
0.5603 Remote Similarity NPD4832 Approved
0.5603 Remote Similarity NPD4831 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