Structure

Physi-Chem Properties

Molecular Weight:  465.27
Volume:  459.509
LogP:  0.955
LogD:  1.93
LogS:  -3.738
# Rotatable Bonds:  6
TPSA:  97.69
# H-Bond Aceptor:  8
# H-Bond Donor:  2
# Rings:  6
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.547
Synthetic Accessibility Score:  7.266
Fsp3:  0.96
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.459
MDCK Permeability:  7.081252260832116e-05
Pgp-inhibitor:  0.787
Pgp-substrate:  0.995
Human Intestinal Absorption (HIA):  0.944
20% Bioavailability (F20%):  0.221
30% Bioavailability (F30%):  0.911

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.193
Plasma Protein Binding (PPB):  25.68700408935547%
Volume Distribution (VD):  0.705
Pgp-substrate:  72.12362670898438%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.976
CYP2C19-inhibitor:  0.002
CYP2C19-substrate:  0.512
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.006
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.147
CYP3A4-inhibitor:  0.079
CYP3A4-substrate:  0.449

ADMET: Excretion

Clearance (CL):  5.33
Half-life (T1/2):  0.23

ADMET: Toxicity

hERG Blockers:  0.113
Human Hepatotoxicity (H-HT):  0.37
Drug-inuced Liver Injury (DILI):  0.076
AMES Toxicity:  0.179
Rat Oral Acute Toxicity:  0.254
Maximum Recommended Daily Dose:  0.022
Skin Sensitization:  0.922
Carcinogencity:  0.072
Eye Corrosion:  0.114
Eye Irritation:  0.012
Respiratory Toxicity:  0.988

Download Data

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

  Natural Product: NPC474210

Natural Product ID:  NPC474210
Common Name*:   Lycoctonal
IUPAC Name:   n.a.
Synonyms:   Lycoctonal
Standard InCHIKey:  ISNYWFKBCCHLMO-NUBXAFMHSA-N
Standard InCHI:  InChI=1S/C25H39NO7/c1-6-26-11-22(12-27)8-7-16(31-3)24-14-9-13-15(30-2)10-23(28,17(14)18(13)32-4)25(29,21(24)26)20(33-5)19(22)24/h12-21,28-29H,6-11H2,1-5H3/t13-,14-,15+,16+,17?,18+,19-,20+,21+,22+,23-,24+,25+/m1/s1
SMILES:  CO[C@H]1C[C@@]2(O)C3[C@H]([C@@H]1C[C@H]3[C@@]13[C@H]4[C@@]2(O)[C@@H](OC)[C@@H]1[C@@](CN4CC)(C=O)CC[C@@H]3OC)OC
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL463512
PubChem CID:   44566473
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001551] Diterpenoids
          • [CHEMONTID:0003788] Aconitane-type diterpenoid alkaloids

*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
NPO33014 delphinium cashmirianum Species Ranunculaceae Eukaryota n.a. n.a. n.a. PMID[541686]

☑ 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
NPT419 Organism Oryctolagus cuniculus Oryctolagus cuniculus Activity = -3.0 bpm PMID[512660]
NPT419 Organism Oryctolagus cuniculus Oryctolagus cuniculus Activity = 0.0 bpm PMID[512660]
NPT419 Organism Oryctolagus cuniculus Oryctolagus cuniculus Activity = -5.0 bpm PMID[512660]
NPT419 Organism Oryctolagus cuniculus Oryctolagus cuniculus Activity = -10.0 bpm PMID[512660]

☑ 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 NPC474210 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
0.872 High Similarity NPC208118
0.872 High Similarity NPC99905
0.872 High Similarity NPC96080
0.8605 High Similarity NPC476501
0.8538 High Similarity NPC476497
0.8413 Intermediate Similarity NPC475887
0.8195 Intermediate Similarity NPC476967
0.8 Intermediate Similarity NPC139778
0.7985 Intermediate Similarity NPC212106
0.776 Intermediate Similarity NPC48127
0.776 Intermediate Similarity NPC8009
0.776 Intermediate Similarity NPC267217
0.776 Intermediate Similarity NPC83047
0.7424 Intermediate Similarity NPC476502
0.7163 Intermediate Similarity NPC309249
0.7029 Intermediate Similarity NPC238323
0.6835 Remote Similarity NPC470594
0.6835 Remote Similarity NPC470593
0.6765 Remote Similarity NPC28224
0.6739 Remote Similarity NPC221196
0.6739 Remote Similarity NPC39485
0.6667 Remote Similarity NPC220111
0.6508 Remote Similarity NPC312637
0.6496 Remote Similarity NPC34977
0.6496 Remote Similarity NPC246399
0.6438 Remote Similarity NPC280903
0.6438 Remote Similarity NPC470537
0.6434 Remote Similarity NPC476504
0.6414 Remote Similarity NPC476503
0.6405 Remote Similarity NPC88943
0.6395 Remote Similarity NPC477352
0.6343 Remote Similarity NPC97336
0.6316 Remote Similarity NPC178853
0.6304 Remote Similarity NPC287764
0.6242 Remote Similarity NPC956
0.6225 Remote Similarity NPC262050
0.6212 Remote Similarity NPC471241
0.62 Remote Similarity NPC478139
0.6197 Remote Similarity NPC202722
0.6197 Remote Similarity NPC471845
0.6197 Remote Similarity NPC471846
0.6197 Remote Similarity NPC39041
0.6197 Remote Similarity NPC241294
0.6188 Remote Similarity NPC40539
0.6183 Remote Similarity NPC174117
0.6176 Remote Similarity NPC475239
0.6154 Remote Similarity NPC163578
0.6154 Remote Similarity NPC108276
0.6136 Remote Similarity NPC116683
0.6127 Remote Similarity NPC476499
0.6127 Remote Similarity NPC135431
0.6127 Remote Similarity NPC79193
0.6122 Remote Similarity NPC473477
0.612 Remote Similarity NPC205
0.612 Remote Similarity NPC184195
0.612 Remote Similarity NPC172769
0.612 Remote Similarity NPC166521
0.612 Remote Similarity NPC124690
0.612 Remote Similarity NPC281470
0.609 Remote Similarity NPC292819
0.6084 Remote Similarity NPC209252
0.6058 Remote Similarity NPC100078
0.6047 Remote Similarity NPC135005
0.6029 Remote Similarity NPC470592
0.6029 Remote Similarity NPC470172
0.6026 Remote Similarity NPC25327
0.6026 Remote Similarity NPC470539
0.6016 Remote Similarity NPC263802
0.6014 Remote Similarity NPC471844
0.6014 Remote Similarity NPC470116
0.6014 Remote Similarity NPC470115
0.6014 Remote Similarity NPC166079
0.6 Remote Similarity NPC473994
0.5987 Remote Similarity NPC201359
0.5986 Remote Similarity NPC477489
0.5986 Remote Similarity NPC477492
0.5986 Remote Similarity NPC476498
0.5985 Remote Similarity NPC471253
0.5985 Remote Similarity NPC34562
0.5985 Remote Similarity NPC473406
0.5985 Remote Similarity NPC477495
0.5985 Remote Similarity NPC107385
0.5972 Remote Similarity NPC475490
0.5972 Remote Similarity NPC470538
0.5972 Remote Similarity NPC476955
0.5944 Remote Similarity NPC97002
0.5942 Remote Similarity NPC470167
0.5942 Remote Similarity NPC327093
0.594 Remote Similarity NPC17336
0.5938 Remote Similarity NPC80700
0.5938 Remote Similarity NPC476726
0.5938 Remote Similarity NPC476727
0.5938 Remote Similarity NPC472272
0.5929 Remote Similarity NPC470595
0.5926 Remote Similarity NPC253995
0.5923 Remote Similarity NPC61688
0.592 Remote Similarity NPC109533
0.5915 Remote Similarity NPC473062
0.5912 Remote Similarity NPC471254
0.5912 Remote Similarity NPC213528
0.5912 Remote Similarity NPC244969
0.5909 Remote Similarity NPC161035
0.5907 Remote Similarity NPC326895
0.5899 Remote Similarity NPC215408
0.5899 Remote Similarity NPC306776
0.5896 Remote Similarity NPC476728
0.5894 Remote Similarity NPC476951
0.5878 Remote Similarity NPC77756
0.5876 Remote Similarity NPC476495
0.5876 Remote Similarity NPC106840
0.5876 Remote Similarity NPC94687
0.5873 Remote Similarity NPC317066
0.5873 Remote Similarity NPC268040
0.5871 Remote Similarity NPC477072
0.5865 Remote Similarity NPC470424
0.5862 Remote Similarity NPC271115
0.5852 Remote Similarity NPC472273
0.5846 Remote Similarity NPC476496
0.5846 Remote Similarity NPC203170
0.5839 Remote Similarity NPC477172
0.5839 Remote Similarity NPC475518
0.5839 Remote Similarity NPC298266
0.5839 Remote Similarity NPC259654
0.5821 Remote Similarity NPC155985
0.5821 Remote Similarity NPC223590
0.5821 Remote Similarity NPC305808
0.5816 Remote Similarity NPC475319
0.5816 Remote Similarity NPC92890
0.5816 Remote Similarity NPC202898
0.5813 Remote Similarity NPC106593
0.5809 Remote Similarity NPC472144
0.5804 Remote Similarity NPC469824
0.5797 Remote Similarity NPC287638
0.5797 Remote Similarity NPC194750
0.5797 Remote Similarity NPC233274
0.5789 Remote Similarity NPC476189
0.5781 Remote Similarity NPC50438
0.5778 Remote Similarity NPC289140
0.5778 Remote Similarity NPC235109
0.5775 Remote Similarity NPC273002
0.5775 Remote Similarity NPC92297
0.5775 Remote Similarity NPC233433
0.5775 Remote Similarity NPC473817
0.5775 Remote Similarity NPC94086
0.5775 Remote Similarity NPC220836
0.5769 Remote Similarity NPC202937
0.5766 Remote Similarity NPC41843
0.5766 Remote Similarity NPC201712
0.5766 Remote Similarity NPC20028
0.5764 Remote Similarity NPC124358
0.5753 Remote Similarity NPC165396
0.5747 Remote Similarity NPC473040
0.5746 Remote Similarity NPC470423
0.5745 Remote Similarity NPC203974
0.5745 Remote Similarity NPC317534
0.5745 Remote Similarity NPC46981
0.5743 Remote Similarity NPC475340
0.5742 Remote Similarity NPC139585
0.5736 Remote Similarity NPC266651
0.5735 Remote Similarity NPC472145
0.5725 Remote Similarity NPC226491
0.5725 Remote Similarity NPC476435
0.5725 Remote Similarity NPC477614
0.5724 Remote Similarity NPC477963
0.5724 Remote Similarity NPC478137
0.5714 Remote Similarity NPC470596
0.5714 Remote Similarity NPC8325
0.5714 Remote Similarity NPC179429
0.5714 Remote Similarity NPC470609
0.5714 Remote Similarity NPC328737
0.5707 Remote Similarity NPC473667
0.5705 Remote Similarity NPC88190
0.5704 Remote Similarity NPC82633
0.5704 Remote Similarity NPC215570
0.5703 Remote Similarity NPC269684
0.5703 Remote Similarity NPC327451
0.5693 Remote Similarity NPC475249
0.5693 Remote Similarity NPC476294
0.5692 Remote Similarity NPC131365
0.5692 Remote Similarity NPC474448
0.5687 Remote Similarity NPC265908
0.5683 Remote Similarity NPC476755
0.5683 Remote Similarity NPC310031
0.5683 Remote Similarity NPC80191
0.5682 Remote Similarity NPC24705
0.5682 Remote Similarity NPC56962
0.568 Remote Similarity NPC67657
0.568 Remote Similarity NPC18857
0.5679 Remote Similarity NPC803
0.5676 Remote Similarity NPC96731
0.5672 Remote Similarity NPC277774
0.5664 Remote Similarity NPC228190
0.5664 Remote Similarity NPC227879
0.5664 Remote Similarity NPC208333
0.5664 Remote Similarity NPC236753
0.5662 Remote Similarity NPC156377
0.5662 Remote Similarity NPC163685
0.5662 Remote Similarity NPC475785
0.5658 Remote Similarity NPC473255
0.5649 Remote Similarity NPC5943

  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 NPC474210 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
0.7 Intermediate Similarity NPD6920 Discontinued
0.6567 Remote Similarity NPD7646 Clinical (unspecified phase)
0.6547 Remote Similarity NPD6940 Discontinued
0.6493 Remote Similarity NPD8040 Discontinued
0.6397 Remote Similarity NPD6415 Discontinued
0.6343 Remote Similarity NPD7987 Approved
0.6343 Remote Similarity NPD7912 Approved
0.6343 Remote Similarity NPD7986 Approved
0.6343 Remote Similarity NPD7911 Approved
0.6312 Remote Similarity NPD7754 Approved
0.6312 Remote Similarity NPD7755 Approved
0.6204 Remote Similarity NPD7990 Approved
0.6204 Remote Similarity NPD7989 Approved
0.617 Remote Similarity NPD8298 Phase 2
0.6139 Remote Similarity NPD5193 Discontinued
0.6119 Remote Similarity NPD8418 Phase 2
0.6099 Remote Similarity NPD8077 Approved
0.6099 Remote Similarity NPD8078 Approved
0.6061 Remote Similarity NPD7991 Discontinued
0.5986 Remote Similarity NPD6921 Approved
0.5929 Remote Similarity NPD8174 Phase 2
0.5857 Remote Similarity NPD8307 Discontinued
0.5857 Remote Similarity NPD8140 Approved
0.5833 Remote Similarity NPD7497 Discontinued
0.5827 Remote Similarity NPD8170 Clinical (unspecified phase)
0.5705 Remote Similarity NPD8345 Approved
0.5705 Remote Similarity NPD8346 Approved
0.5705 Remote Similarity NPD8347 Approved
0.5625 Remote Similarity NPD8087 Discontinued
0.562 Remote Similarity NPD7920 Phase 3
0.562 Remote Similarity NPD7919 Phase 3

  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