Structure

Physi-Chem Properties

Molecular Weight:  277.17
Volume:  295.001
LogP:  2.372
LogD:  2.874
LogS:  -2.467
# Rotatable Bonds:  2
TPSA:  62.46
# H-Bond Aceptor:  4
# H-Bond Donor:  2
# Rings:  2
# Heavy Atoms:  4

MedChem Properties

QED Drug-Likeness Score:  0.645
Synthetic Accessibility Score:  4.529
Fsp3:  0.562
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  1
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.758
MDCK Permeability:  2.432864494039677e-05
Pgp-inhibitor:  0.001
Pgp-substrate:  0.019
Human Intestinal Absorption (HIA):  0.004
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.002

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.187
Plasma Protein Binding (PPB):  77.96402740478516%
Volume Distribution (VD):  0.866
Pgp-substrate:  28.9942626953125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.266
CYP1A2-substrate:  0.612
CYP2C19-inhibitor:  0.451
CYP2C19-substrate:  0.538
CYP2C9-inhibitor:  0.783
CYP2C9-substrate:  0.848
CYP2D6-inhibitor:  0.018
CYP2D6-substrate:  0.108
CYP3A4-inhibitor:  0.926
CYP3A4-substrate:  0.298

ADMET: Excretion

Clearance (CL):  5.199
Half-life (T1/2):  0.417

ADMET: Toxicity

hERG Blockers:  0.014
Human Hepatotoxicity (H-HT):  0.173
Drug-inuced Liver Injury (DILI):  0.159
AMES Toxicity:  0.052
Rat Oral Acute Toxicity:  0.693
Maximum Recommended Daily Dose:  0.824
Skin Sensitization:  0.668
Carcinogencity:  0.48
Eye Corrosion:  0.011
Eye Irritation:  0.124
Respiratory Toxicity:  0.842

Download Data

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

  Natural Product: NPC247316

Natural Product ID:  NPC247316
Common Name*:   Cordypyridone B
IUPAC Name:   3-[(1R,2S,4R,6S)-2-ethenyl-2,4,6-trimethylcyclohexyl]-1,4-dihydroxypyridin-2-one
Synonyms:   8-Methyl Pyridoxatin
Standard InCHIKey:  RUYMPIIPQAXOTF-PSHZPRKYSA-N
Standard InCHI:  InChI=1S/C16H23NO3/c1-5-16(4)9-10(2)8-11(3)14(16)13-12(18)6-7-17(20)15(13)19/h5-7,10-11,14,18,20H,1,8-9H2,2-4H3/t10-,11+,14+,16-/m1/s1
SMILES:  C=C[C@]1(C)C[C@H](C)C[C@@H]([C@H]1c1c(O)ccn(c1=O)O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL453011
PubChem CID:   54706232
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0000089] Pyridines and derivatives
        • [CHEMONTID:0002224] Hydropyridines
          • [CHEMONTID:0001160] Pyridinones

*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
NPO33042 os-f61800 n.a. n.a. n.a. n.a. n.a. n.a. PMID[10075801]

☑ 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
NPT20904 CELL-LINE Hep 3B2 Homo sapiens Activity = 0.3 uM PMID[541634]
NPT20904 CELL-LINE Hep 3B2 Homo sapiens Activity = 46.0 uM PMID[541634]
NPT20904 CELL-LINE Hep 3B2 Homo sapiens Activity = 120.0 mU PMID[541634]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC90 > 20000.0 nM PMID[541634]
NPT757 Organism Plasmodium falciparum 3D7 Plasmodium falciparum 3D7 IC50 = 800.0 nM PMID[541635]

☑ 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 NPC247316 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
0.954 High Similarity NPC473056
0.8077 Intermediate Similarity NPC44733
0.6952 Remote Similarity NPC316730
0.6916 Remote Similarity NPC318544
0.6852 Remote Similarity NPC470073
0.6789 Remote Similarity NPC476328
0.6729 Remote Similarity NPC77703
0.6667 Remote Similarity NPC476276
0.6574 Remote Similarity NPC34193
0.6545 Remote Similarity NPC469958
0.6509 Remote Similarity NPC247220
0.65 Remote Similarity NPC311769
0.65 Remote Similarity NPC182106
0.6495 Remote Similarity NPC469797
0.6495 Remote Similarity NPC469798
0.6491 Remote Similarity NPC143173
0.6489 Remote Similarity NPC476346
0.6481 Remote Similarity NPC477964
0.6452 Remote Similarity NPC56747
0.6452 Remote Similarity NPC180015
0.6452 Remote Similarity NPC109576
0.6452 Remote Similarity NPC130016
0.6449 Remote Similarity NPC184033
0.6422 Remote Similarity NPC474001
0.6372 Remote Similarity NPC470072
0.6364 Remote Similarity NPC469804
0.6364 Remote Similarity NPC469805
0.6364 Remote Similarity NPC469799
0.6364 Remote Similarity NPC469806
0.6364 Remote Similarity NPC152718
0.6364 Remote Similarity NPC226509
0.6344 Remote Similarity NPC133253
0.6339 Remote Similarity NPC185929
0.6339 Remote Similarity NPC476926
0.6337 Remote Similarity NPC76283
0.6316 Remote Similarity NPC175585
0.6311 Remote Similarity NPC259252
0.63 Remote Similarity NPC3856
0.63 Remote Similarity NPC279639
0.6289 Remote Similarity NPC275494
0.6289 Remote Similarity NPC189485
0.6289 Remote Similarity NPC471409
0.625 Remote Similarity NPC1254
0.625 Remote Similarity NPC249312
0.6228 Remote Similarity NPC476920
0.6228 Remote Similarity NPC24596
0.6228 Remote Similarity NPC476918
0.6224 Remote Similarity NPC27817
0.622 Remote Similarity NPC103605
0.622 Remote Similarity NPC81092
0.6216 Remote Similarity NPC58200
0.6211 Remote Similarity NPC329866
0.6211 Remote Similarity NPC474796
0.6211 Remote Similarity NPC474797
0.6198 Remote Similarity NPC477140
0.6198 Remote Similarity NPC477143
0.6196 Remote Similarity NPC260474
0.6196 Remote Similarity NPC188292
0.6196 Remote Similarity NPC310992
0.6195 Remote Similarity NPC230677
0.617 Remote Similarity NPC21944
0.6168 Remote Similarity NPC476754
0.6162 Remote Similarity NPC287063
0.6146 Remote Similarity NPC473171
0.6121 Remote Similarity NPC476290
0.6121 Remote Similarity NPC72688
0.6121 Remote Similarity NPC63511
0.6117 Remote Similarity NPC157479
0.61 Remote Similarity NPC475863
0.61 Remote Similarity NPC225515
0.61 Remote Similarity NPC470034
0.6087 Remote Similarity NPC476919
0.6082 Remote Similarity NPC469793
0.6082 Remote Similarity NPC469796
0.6082 Remote Similarity NPC19907
0.6078 Remote Similarity NPC87552
0.6075 Remote Similarity NPC476752
0.6075 Remote Similarity NPC476753
0.6058 Remote Similarity NPC476293
0.6044 Remote Similarity NPC251118
0.604 Remote Similarity NPC477583
0.6022 Remote Similarity NPC87141
0.602 Remote Similarity NPC91665
0.602 Remote Similarity NPC266193
0.602 Remote Similarity NPC257666
0.6019 Remote Similarity NPC147513
0.6017 Remote Similarity NPC476269
0.6 Remote Similarity NPC472166
0.6 Remote Similarity NPC54123
0.5979 Remote Similarity NPC469803
0.5977 Remote Similarity NPC115385
0.5965 Remote Similarity NPC476921
0.5962 Remote Similarity NPC472136
0.596 Remote Similarity NPC179028
0.5957 Remote Similarity NPC256846
0.5957 Remote Similarity NPC139397
0.5955 Remote Similarity NPC127582
0.5943 Remote Similarity NPC36668
0.5943 Remote Similarity NPC118011
0.5943 Remote Similarity NPC474918
0.5941 Remote Similarity NPC4166
0.5941 Remote Similarity NPC477582
0.5941 Remote Similarity NPC121984
0.5934 Remote Similarity NPC469662
0.5934 Remote Similarity NPC475124
0.5934 Remote Similarity NPC285371
0.5934 Remote Similarity NPC150162
0.5918 Remote Similarity NPC180886
0.5918 Remote Similarity NPC263582
0.5918 Remote Similarity NPC110725
0.5917 Remote Similarity NPC176336
0.5905 Remote Similarity NPC75315
0.5905 Remote Similarity NPC163016
0.5902 Remote Similarity NPC474006
0.59 Remote Similarity NPC474113
0.5895 Remote Similarity NPC251929
0.5895 Remote Similarity NPC265782
0.5895 Remote Similarity NPC307176
0.5895 Remote Similarity NPC2634
0.5895 Remote Similarity NPC260040
0.5889 Remote Similarity NPC60565
0.5889 Remote Similarity NPC469728
0.5882 Remote Similarity NPC268122
0.5882 Remote Similarity NPC472867
0.5882 Remote Similarity NPC3511
0.5882 Remote Similarity NPC142253
0.5882 Remote Similarity NPC472239
0.5882 Remote Similarity NPC311092
0.5882 Remote Similarity NPC477581
0.5882 Remote Similarity NPC215474
0.5877 Remote Similarity NPC474563
0.5876 Remote Similarity NPC237591
0.5876 Remote Similarity NPC3753
0.587 Remote Similarity NPC268039
0.5865 Remote Similarity NPC33881
0.5865 Remote Similarity NPC476426
0.5859 Remote Similarity NPC61952
0.5859 Remote Similarity NPC97377
0.5851 Remote Similarity NPC155198
0.5849 Remote Similarity NPC72397
0.5847 Remote Similarity NPC328052
0.5843 Remote Similarity NPC472304
0.5843 Remote Similarity NPC276764
0.5842 Remote Similarity NPC108955
0.5842 Remote Similarity NPC26139
0.5842 Remote Similarity NPC476560
0.5842 Remote Similarity NPC250632
0.5842 Remote Similarity NPC476809
0.5841 Remote Similarity NPC476922
0.5833 Remote Similarity NPC115023
0.5833 Remote Similarity NPC470078
0.5833 Remote Similarity NPC5701
0.5833 Remote Similarity NPC473986
0.5833 Remote Similarity NPC190035
0.5833 Remote Similarity NPC181204
0.5833 Remote Similarity NPC474018
0.5833 Remote Similarity NPC305501
0.5833 Remote Similarity NPC204341
0.5825 Remote Similarity NPC118423
0.5825 Remote Similarity NPC477584
0.5825 Remote Similarity NPC474790
0.5825 Remote Similarity NPC41539
0.5825 Remote Similarity NPC21667
0.5825 Remote Similarity NPC474976
0.5824 Remote Similarity NPC202118
0.5824 Remote Similarity NPC288253
0.5824 Remote Similarity NPC197238
0.582 Remote Similarity NPC476190
0.5816 Remote Similarity NPC476795
0.5816 Remote Similarity NPC476844
0.5816 Remote Similarity NPC65650
0.581 Remote Similarity NPC194417
0.5806 Remote Similarity NPC255781
0.5806 Remote Similarity NPC259156
0.5806 Remote Similarity NPC242945
0.58 Remote Similarity NPC62336
0.58 Remote Similarity NPC198240
0.5794 Remote Similarity NPC472688
0.5794 Remote Similarity NPC472676
0.5784 Remote Similarity NPC6663
0.5784 Remote Similarity NPC55869
0.5784 Remote Similarity NPC472684
0.5784 Remote Similarity NPC99308
0.5784 Remote Similarity NPC189237
0.5784 Remote Similarity NPC44963
0.578 Remote Similarity NPC242069
0.578 Remote Similarity NPC469939
0.5778 Remote Similarity NPC176621
0.5773 Remote Similarity NPC251705
0.5773 Remote Similarity NPC470044
0.5773 Remote Similarity NPC470045
0.5773 Remote Similarity NPC247586
0.5773 Remote Similarity NPC303613
0.5773 Remote Similarity NPC153660
0.5773 Remote Similarity NPC474228
0.5769 Remote Similarity NPC178025
0.5769 Remote Similarity NPC135639
0.5769 Remote Similarity NPC61321
0.5769 Remote Similarity NPC78058
0.5769 Remote Similarity NPC181743

  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 NPC247316 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
0.6703 Remote Similarity NPD815 Approved
0.6703 Remote Similarity NPD816 Approved
0.6476 Remote Similarity NPD5769 Clinical (unspecified phase)
0.6339 Remote Similarity NPD7333 Discontinued
0.63 Remote Similarity NPD3527 Clinical (unspecified phase)
0.6211 Remote Similarity NPD4687 Approved
0.6211 Remote Similarity NPD4058 Approved
0.6042 Remote Similarity NPD5733 Approved
0.6 Remote Similarity NPD5276 Approved
0.5957 Remote Similarity NPD4137 Phase 3
0.5895 Remote Similarity NPD4691 Approved
0.5895 Remote Similarity NPD4747 Approved
0.581 Remote Similarity NPD4519 Discontinued
0.581 Remote Similarity NPD4623 Approved
0.58 Remote Similarity NPD1402 Approved
0.5784 Remote Similarity NPD8028 Phase 2
0.5758 Remote Similarity NPD2754 Discontinued
0.5752 Remote Similarity NPD6404 Discontinued
0.5741 Remote Similarity NPD4096 Approved
0.5686 Remote Similarity NPD4695 Discontinued
0.566 Remote Similarity NPD4694 Approved
0.566 Remote Similarity NPD5280 Approved
0.5648 Remote Similarity NPD7285 Clinical (unspecified phase)
0.5644 Remote Similarity NPD3617 Approved
0.5625 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5615 Remote Similarity NPD6330 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