Structure

Physi-Chem Properties

Molecular Weight:  236.18
Volume:  269.111
LogP:  3.214
LogD:  2.884
LogS:  -3.101
# Rotatable Bonds:  0
TPSA:  34.14
# H-Bond Aceptor:  2
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.601
Synthetic Accessibility Score:  4.027
Fsp3:  0.733
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -4.579
MDCK Permeability:  1.810607864172198e-05
Pgp-inhibitor:  0.879
Pgp-substrate:  0.007
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  0.804
30% Bioavailability (F30%):  0.062

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.938
Plasma Protein Binding (PPB):  88.8504867553711%
Volume Distribution (VD):  0.567
Pgp-substrate:  12.26370620727539%

ADMET: Metabolism

CYP1A2-inhibitor:  0.263
CYP1A2-substrate:  0.704
CYP2C19-inhibitor:  0.552
CYP2C19-substrate:  0.863
CYP2C9-inhibitor:  0.306
CYP2C9-substrate:  0.333
CYP2D6-inhibitor:  0.034
CYP2D6-substrate:  0.313
CYP3A4-inhibitor:  0.138
CYP3A4-substrate:  0.469

ADMET: Excretion

Clearance (CL):  13.383
Half-life (T1/2):  0.852

ADMET: Toxicity

hERG Blockers:  0.008
Human Hepatotoxicity (H-HT):  0.169
Drug-inuced Liver Injury (DILI):  0.414
AMES Toxicity:  0.2
Rat Oral Acute Toxicity:  0.459
Maximum Recommended Daily Dose:  0.25
Skin Sensitization:  0.904
Carcinogencity:  0.707
Eye Corrosion:  0.914
Eye Irritation:  0.904
Respiratory Toxicity:  0.961

Download Data

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

  Natural Product: NPC63396

Natural Product ID:  NPC63396
Common Name*:   KDPFMRXIVDLQKX-YCBFNFSOSA-N
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  KDPFMRXIVDLQKX-YCBFNFSOSA-N
Standard InCHI:  InChI=1S/C15H24O2/c1-10(2)13-9-14(16)12(4)7-5-6-11(3)8-15(13)17/h6,10,12-13H,5,7-9H2,1-4H3/b11-6-/t12-,13+/m1/s1
SMILES:  CC(C)[C@@H]1CC(=O)[C@H](C)CC/C=C(/C)CC1=O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL116790
PubChem CID:   NA
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0000259] Prenol lipids
        • [CHEMONTID:0001550] Sesquiterpenoids
          • [CHEMONTID:0002456] Germacrane sesquiterpenoids

*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
NPO33283 zedoariae rhizoma n.a. n.a. n.a. n.a. n.a. n.a. PMID[9871681]

☑ 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
NPT32 Organism Mus musculus Mus musculus Inhibition = 59.3 % PMID[523780]
NPT32 Organism Mus musculus Mus musculus Inhibition = 58.4 % PMID[523780]
NPT29 Organism Rattus norvegicus Rattus norvegicus Inhibition = 44.6 % PMID[523780]
NPT32 Organism Mus musculus Mus musculus Inhibition = 41.9 % PMID[523780]

☑ 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 NPC63396 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 NPC202850
0.9423 High Similarity NPC275472
0.94 High Similarity NPC27438
0.8393 Intermediate Similarity NPC193695
0.8333 Intermediate Similarity NPC474141
0.8103 Intermediate Similarity NPC259261
0.807 Intermediate Similarity NPC55004
0.807 Intermediate Similarity NPC49575
0.807 Intermediate Similarity NPC230823
0.807 Intermediate Similarity NPC267626
0.8 Intermediate Similarity NPC268564
0.7931 Intermediate Similarity NPC30215
0.7931 Intermediate Similarity NPC94991
0.7931 Intermediate Similarity NPC266295
0.7903 Intermediate Similarity NPC197089
0.7895 Intermediate Similarity NPC20603
0.7869 Intermediate Similarity NPC473902
0.7833 Intermediate Similarity NPC475795
0.7833 Intermediate Similarity NPC60565
0.7797 Intermediate Similarity NPC143834
0.7797 Intermediate Similarity NPC285594
0.7797 Intermediate Similarity NPC96551
0.7797 Intermediate Similarity NPC276764
0.7797 Intermediate Similarity NPC472304
0.7778 Intermediate Similarity NPC32351
0.7759 Intermediate Similarity NPC115385
0.7736 Intermediate Similarity NPC91962
0.7679 Intermediate Similarity NPC45283
0.7667 Intermediate Similarity NPC127582
0.7667 Intermediate Similarity NPC25853
0.7636 Intermediate Similarity NPC236623
0.7581 Intermediate Similarity NPC212210
0.7547 Intermediate Similarity NPC262558
0.7547 Intermediate Similarity NPC8610
0.7541 Intermediate Similarity NPC97322
0.7541 Intermediate Similarity NPC213152
0.75 Intermediate Similarity NPC475523
0.75 Intermediate Similarity NPC471751
0.746 Intermediate Similarity NPC251118
0.746 Intermediate Similarity NPC470329
0.7458 Intermediate Similarity NPC192427
0.7455 Intermediate Similarity NPC116906
0.7419 Intermediate Similarity NPC167256
0.7419 Intermediate Similarity NPC32285
0.7419 Intermediate Similarity NPC165695
0.7419 Intermediate Similarity NPC197238
0.7419 Intermediate Similarity NPC202118
0.7419 Intermediate Similarity NPC288253
0.7414 Intermediate Similarity NPC200258
0.7368 Intermediate Similarity NPC296311
0.7333 Intermediate Similarity NPC311852
0.7333 Intermediate Similarity NPC27610
0.7333 Intermediate Similarity NPC56905
0.7308 Intermediate Similarity NPC301972
0.7302 Intermediate Similarity NPC475124
0.7302 Intermediate Similarity NPC150162
0.7302 Intermediate Similarity NPC6697
0.7302 Intermediate Similarity NPC285371
0.7302 Intermediate Similarity NPC469662
0.7288 Intermediate Similarity NPC473733
0.7273 Intermediate Similarity NPC145311
0.7222 Intermediate Similarity NPC276009
0.7222 Intermediate Similarity NPC236355
0.7222 Intermediate Similarity NPC195246
0.7222 Intermediate Similarity NPC14917
0.7222 Intermediate Similarity NPC22098
0.7222 Intermediate Similarity NPC4079
0.7206 Intermediate Similarity NPC275098
0.7164 Intermediate Similarity NPC260040
0.7143 Intermediate Similarity NPC176819
0.7143 Intermediate Similarity NPC58970
0.7143 Intermediate Similarity NPC163984
0.7121 Intermediate Similarity NPC188292
0.7121 Intermediate Similarity NPC87141
0.7121 Intermediate Similarity NPC260474
0.7121 Intermediate Similarity NPC155198
0.7059 Intermediate Similarity NPC474562
0.7049 Intermediate Similarity NPC308108
0.7049 Intermediate Similarity NPC170799
0.7018 Intermediate Similarity NPC64866
0.7015 Intermediate Similarity NPC144511
0.7015 Intermediate Similarity NPC286814
0.7015 Intermediate Similarity NPC256846
0.7015 Intermediate Similarity NPC296522
0.7015 Intermediate Similarity NPC469677
0.7015 Intermediate Similarity NPC139397
0.7015 Intermediate Similarity NPC61702
0.7015 Intermediate Similarity NPC162867
0.697 Remote Similarity NPC290350
0.697 Remote Similarity NPC278895
0.697 Remote Similarity NPC4370
0.6923 Remote Similarity NPC474304
0.6923 Remote Similarity NPC474329
0.6912 Remote Similarity NPC2634
0.6912 Remote Similarity NPC265782
0.6912 Remote Similarity NPC307176
0.6912 Remote Similarity NPC40574
0.6912 Remote Similarity NPC251929
0.6909 Remote Similarity NPC100380
0.6897 Remote Similarity NPC216407
0.6866 Remote Similarity NPC142754
0.6866 Remote Similarity NPC469688
0.6866 Remote Similarity NPC310992
0.6866 Remote Similarity NPC82477
0.6866 Remote Similarity NPC476614
0.6866 Remote Similarity NPC20610
0.6866 Remote Similarity NPC39157
0.6866 Remote Similarity NPC296697
0.6857 Remote Similarity NPC309852
0.6852 Remote Similarity NPC25771
0.6842 Remote Similarity NPC228776
0.6842 Remote Similarity NPC15325
0.6833 Remote Similarity NPC188789
0.6833 Remote Similarity NPC477984
0.6825 Remote Similarity NPC40206
0.6818 Remote Similarity NPC323005
0.6818 Remote Similarity NPC126899
0.6818 Remote Similarity NPC154728
0.6818 Remote Similarity NPC304665
0.6812 Remote Similarity NPC181204
0.6812 Remote Similarity NPC21944
0.6812 Remote Similarity NPC190035
0.6812 Remote Similarity NPC133253
0.6812 Remote Similarity NPC54123
0.6812 Remote Similarity NPC129665
0.68 Remote Similarity NPC185839
0.678 Remote Similarity NPC23117
0.6769 Remote Similarity NPC4638
0.6769 Remote Similarity NPC234767
0.6765 Remote Similarity NPC469914
0.6765 Remote Similarity NPC182815
0.6765 Remote Similarity NPC477449
0.6765 Remote Similarity NPC477448
0.6761 Remote Similarity NPC155587
0.6761 Remote Similarity NPC244166
0.6727 Remote Similarity NPC166788
0.6724 Remote Similarity NPC477458
0.6716 Remote Similarity NPC60120
0.6716 Remote Similarity NPC20181
0.6716 Remote Similarity NPC220210
0.6714 Remote Similarity NPC474228
0.6714 Remote Similarity NPC107783
0.6714 Remote Similarity NPC300940
0.6714 Remote Similarity NPC130016
0.6714 Remote Similarity NPC470237
0.6714 Remote Similarity NPC303613
0.6714 Remote Similarity NPC109576
0.6714 Remote Similarity NPC92909
0.6714 Remote Similarity NPC180015
0.6714 Remote Similarity NPC474488
0.6714 Remote Similarity NPC56747
0.6667 Remote Similarity NPC472955
0.6667 Remote Similarity NPC155880
0.6667 Remote Similarity NPC214770
0.6667 Remote Similarity NPC209431
0.6667 Remote Similarity NPC95581
0.6667 Remote Similarity NPC268039
0.6667 Remote Similarity NPC180840
0.6667 Remote Similarity NPC106819
0.6667 Remote Similarity NPC92863
0.6667 Remote Similarity NPC292463
0.6667 Remote Similarity NPC35734
0.6667 Remote Similarity NPC151045
0.6667 Remote Similarity NPC100809
0.6667 Remote Similarity NPC282593
0.6667 Remote Similarity NPC246722
0.6667 Remote Similarity NPC477856
0.6667 Remote Similarity NPC86538
0.6667 Remote Similarity NPC159577
0.662 Remote Similarity NPC206875
0.662 Remote Similarity NPC20025
0.662 Remote Similarity NPC329866
0.662 Remote Similarity NPC474797
0.662 Remote Similarity NPC474796
0.662 Remote Similarity NPC469691
0.662 Remote Similarity NPC167049
0.6618 Remote Similarity NPC469679
0.6615 Remote Similarity NPC472306
0.6613 Remote Similarity NPC165808
0.661 Remote Similarity NPC22182
0.661 Remote Similarity NPC68014
0.6607 Remote Similarity NPC471752
0.6604 Remote Similarity NPC120926
0.6604 Remote Similarity NPC218918
0.66 Remote Similarity NPC38497
0.6571 Remote Similarity NPC304983
0.6571 Remote Similarity NPC469737
0.6571 Remote Similarity NPC470078
0.6571 Remote Similarity NPC29328
0.6571 Remote Similarity NPC5701
0.6571 Remote Similarity NPC288667
0.6571 Remote Similarity NPC115023
0.6552 Remote Similarity NPC474391
0.6538 Remote Similarity NPC141634
0.6528 Remote Similarity NPC472256
0.6528 Remote Similarity NPC473171
0.6528 Remote Similarity NPC475771
0.6528 Remote Similarity NPC114236
0.6528 Remote Similarity NPC469669
0.6528 Remote Similarity NPC469678

  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 NPC63396 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
0.7049 Intermediate Similarity NPD287 Approved
0.7015 Intermediate Similarity NPD4137 Phase 3
0.6912 Remote Similarity NPD4747 Approved
0.6912 Remote Similarity NPD4691 Approved
0.6866 Remote Similarity NPD3621 Clinical (unspecified phase)
0.6818 Remote Similarity NPD7331 Phase 2
0.6812 Remote Similarity NPD5276 Approved
0.662 Remote Similarity NPD5733 Approved
0.662 Remote Similarity NPD4687 Approved
0.662 Remote Similarity NPD4058 Approved
0.6538 Remote Similarity NPD5783 Phase 3
0.6418 Remote Similarity NPD7341 Phase 2
0.6167 Remote Similarity NPD29 Approved
0.6167 Remote Similarity NPD28 Approved
0.6104 Remote Similarity NPD4695 Discontinued
0.6053 Remote Similarity NPD5784 Clinical (unspecified phase)
0.6032 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5968 Remote Similarity NPD3172 Approved
0.5949 Remote Similarity NPD3667 Approved
0.5949 Remote Similarity NPD4223 Phase 3
0.5949 Remote Similarity NPD4221 Approved
0.5897 Remote Similarity NPD5368 Approved
0.5882 Remote Similarity NPD2664 Clinical (unspecified phase)
0.5875 Remote Similarity NPD3527 Clinical (unspecified phase)
0.5873 Remote Similarity NPD4266 Approved
0.5873 Remote Similarity NPD3195 Phase 2
0.5873 Remote Similarity NPD3194 Approved
0.5873 Remote Similarity NPD3196 Approved
0.5862 Remote Similarity NPD3174 Discontinued
0.5857 Remote Similarity NPD6108 Clinical (unspecified phase)
0.5849 Remote Similarity NPD319 Phase 1
0.5823 Remote Similarity NPD5369 Approved
0.5823 Remote Similarity NPD8028 Phase 2
0.5802 Remote Similarity NPD4786 Approved
0.5802 Remote Similarity NPD4197 Approved
0.5802 Remote Similarity NPD3665 Phase 1
0.5802 Remote Similarity NPD3666 Approved
0.5802 Remote Similarity NPD3133 Approved
0.5802 Remote Similarity NPD3668 Phase 3
0.5763 Remote Similarity NPD344 Approved
0.5763 Remote Similarity NPD343 Approved
0.5763 Remote Similarity NPD345 Approved
0.575 Remote Similarity NPD4269 Approved
0.575 Remote Similarity NPD6435 Approved
0.575 Remote Similarity NPD4270 Approved
0.5732 Remote Similarity NPD5329 Approved
0.5732 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5696 Remote Similarity NPD4252 Approved
0.5679 Remote Similarity NPD5362 Discontinued
0.5663 Remote Similarity NPD4693 Phase 3
0.5663 Remote Similarity NPD7521 Approved
0.5663 Remote Similarity NPD5205 Approved
0.5663 Remote Similarity NPD4138 Approved
0.5663 Remote Similarity NPD7334 Approved
0.5663 Remote Similarity NPD5280 Approved
0.5663 Remote Similarity NPD5279 Phase 3
0.5663 Remote Similarity NPD4694 Approved
0.5663 Remote Similarity NPD4623 Approved
0.5663 Remote Similarity NPD6098 Approved
0.5663 Remote Similarity NPD4690 Approved
0.5663 Remote Similarity NPD5690 Phase 2
0.5663 Remote Similarity NPD6684 Approved
0.5663 Remote Similarity NPD3618 Phase 1
0.5663 Remote Similarity NPD6409 Approved
0.5663 Remote Similarity NPD4688 Approved
0.5663 Remote Similarity NPD4519 Discontinued
0.5663 Remote Similarity NPD7146 Approved
0.5663 Remote Similarity NPD5330 Approved
0.5663 Remote Similarity NPD4689 Approved
0.5663 Remote Similarity NPD5786 Approved
0.5658 Remote Similarity NPD8039 Approved
0.5641 Remote Similarity NPD3617 Approved
0.5625 Remote Similarity NPD857 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