Structure

Physi-Chem Properties

Molecular Weight:  460.32
Volume:  500.58
LogP:  6.804
LogD:  4.359
LogS:  -6.331
# Rotatable Bonds:  14
TPSA:  61.83
# H-Bond Aceptor:  5
# H-Bond Donor:  0
# Rings:  3
# Heavy Atoms:  5

MedChem Properties

QED Drug-Likeness Score:  0.225
Synthetic Accessibility Score:  4.757
Fsp3:  0.786
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Rejected
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:  -4.762
MDCK Permeability:  4.467631515581161e-05
Pgp-inhibitor:  0.747
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.001
20% Bioavailability (F20%):  0.648
30% Bioavailability (F30%):  0.433

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.065
Plasma Protein Binding (PPB):  99.79520416259766%
Volume Distribution (VD):  1.959
Pgp-substrate:  1.6434794664382935%

ADMET: Metabolism

CYP1A2-inhibitor:  0.035
CYP1A2-substrate:  0.193
CYP2C19-inhibitor:  0.727
CYP2C19-substrate:  0.806
CYP2C9-inhibitor:  0.418
CYP2C9-substrate:  0.337
CYP2D6-inhibitor:  0.839
CYP2D6-substrate:  0.029
CYP3A4-inhibitor:  0.825
CYP3A4-substrate:  0.395

ADMET: Excretion

Clearance (CL):  5.87
Half-life (T1/2):  0.188

ADMET: Toxicity

hERG Blockers:  0.765
Human Hepatotoxicity (H-HT):  0.819
Drug-inuced Liver Injury (DILI):  0.037
AMES Toxicity:  0.166
Rat Oral Acute Toxicity:  0.026
Maximum Recommended Daily Dose:  0.994
Skin Sensitization:  0.986
Carcinogencity:  0.869
Eye Corrosion:  0.105
Eye Irritation:  0.689
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: NPC471552

Natural Product ID:  NPC471552
Common Name*:   [(2R,4R,6S)-11-Oxo-4-Tridecyl-5,7-Dioxadispiro[5.1.5^{8}.2^{6}]Pentadeca-9,12-Dien-2-Yl] Acetate
IUPAC Name:   [(2R,4R,6S)-11-oxo-4-tridecyl-5,7-dioxadispiro[5.1.5^{8}.2^{6}]pentadeca-9,12-dien-2-yl] acetate
Synonyms:  
Standard InCHIKey:  YIZCHFZJRZOMJL-GTNKKZTPSA-N
Standard InCHI:  InChI=1S/C28H44O5/c1-3-4-5-6-7-8-9-10-11-12-13-14-25-21-26(31-23(2)29)22-28(32-25)20-19-27(33-28)17-15-24(30)16-18-27/h15-18,25-26H,3-14,19-22H2,1-2H3/t25-,26-,28+/m1/s1
SMILES:  CCCCCCCCCCCCCC1CC(CC2(O1)CCC3(O2)C=CC(=O)C=C3)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL256501
PubChem CID:   24853672
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000254] Ethers
          • [CHEMONTID:0001656] Acetals
            • [CHEMONTID:0004472] Ketals

*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
NPO17710 Amomum aculeatum Species Zingiberaceae Eukaryota n.a. n.a. n.a. PMID[18260638]
NPO17710 Amomum aculeatum Species Zingiberaceae Eukaryota n.a. leaf n.a. PMID[18260638]
NPO17710 Amomum aculeatum Species Zingiberaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO17710 Amomum aculeatum Species Zingiberaceae 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
NPT1034 Cell Line Lu1 Homo sapiens ED50 = 5.7 uM PMID[542558]
NPT858 Cell Line LNCaP Homo sapiens ED50 = 2.2 uM PMID[542558]
NPT83 Cell Line MCF7 Homo sapiens ED50 = 3.5 uM PMID[542558]

☑ 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 NPC471552 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 NPC473339
0.9241 High Similarity NPC263087
0.9241 High Similarity NPC31019
0.9241 High Similarity NPC106912
0.9241 High Similarity NPC2379
0.9241 High Similarity NPC27314
0.8929 High Similarity NPC471569
0.878 High Similarity NPC473353
0.8608 High Similarity NPC326753
0.7935 Intermediate Similarity NPC266842
0.7802 Intermediate Similarity NPC256368
0.7727 Intermediate Similarity NPC313658
0.7727 Intermediate Similarity NPC316138
0.7667 Intermediate Similarity NPC202886
0.7619 Intermediate Similarity NPC139712
0.7582 Intermediate Similarity NPC477749
0.7556 Intermediate Similarity NPC477748
0.7556 Intermediate Similarity NPC133450
0.75 Intermediate Similarity NPC471494
0.7474 Intermediate Similarity NPC203627
0.7473 Intermediate Similarity NPC177668
0.7471 Intermediate Similarity NPC170286
0.7442 Intermediate Similarity NPC469469
0.7439 Intermediate Similarity NPC477204
0.7416 Intermediate Similarity NPC311163
0.7407 Intermediate Similarity NPC475762
0.7386 Intermediate Similarity NPC475035
0.7386 Intermediate Similarity NPC266718
0.7356 Intermediate Similarity NPC475690
0.734 Intermediate Similarity NPC471362
0.734 Intermediate Similarity NPC471372
0.734 Intermediate Similarity NPC472189
0.7333 Intermediate Similarity NPC199382
0.7317 Intermediate Similarity NPC327383
0.7317 Intermediate Similarity NPC185186
0.7312 Intermediate Similarity NPC238090
0.7312 Intermediate Similarity NPC472196
0.7312 Intermediate Similarity NPC472195
0.7282 Intermediate Similarity NPC471570
0.7263 Intermediate Similarity NPC171598
0.7241 Intermediate Similarity NPC8538
0.7241 Intermediate Similarity NPC184208
0.7234 Intermediate Similarity NPC159698
0.7234 Intermediate Similarity NPC477722
0.7234 Intermediate Similarity NPC88507
0.7222 Intermediate Similarity NPC208473
0.7216 Intermediate Similarity NPC13743
0.7216 Intermediate Similarity NPC98813
0.7209 Intermediate Similarity NPC473981
0.7209 Intermediate Similarity NPC473980
0.72 Intermediate Similarity NPC239961
0.7195 Intermediate Similarity NPC477084
0.7188 Intermediate Similarity NPC472188
0.7176 Intermediate Similarity NPC477203
0.7174 Intermediate Similarity NPC78008
0.716 Intermediate Similarity NPC269841
0.7159 Intermediate Similarity NPC10080
0.7159 Intermediate Similarity NPC123908
0.7143 Intermediate Similarity NPC2313
0.7143 Intermediate Similarity NPC471056
0.7143 Intermediate Similarity NPC327041
0.7143 Intermediate Similarity NPC154132
0.7143 Intermediate Similarity NPC475037
0.7143 Intermediate Similarity NPC119467
0.7143 Intermediate Similarity NPC471637
0.7143 Intermediate Similarity NPC285840
0.7143 Intermediate Similarity NPC57586
0.7143 Intermediate Similarity NPC475157
0.7143 Intermediate Similarity NPC475767
0.7143 Intermediate Similarity NPC475655
0.7143 Intermediate Similarity NPC471055
0.7129 Intermediate Similarity NPC109376
0.7128 Intermediate Similarity NPC471483
0.7125 Intermediate Similarity NPC472266
0.7113 Intermediate Similarity NPC476800
0.7113 Intermediate Similarity NPC65700
0.7113 Intermediate Similarity NPC472186
0.7113 Intermediate Similarity NPC318917
0.7113 Intermediate Similarity NPC471366
0.7111 Intermediate Similarity NPC472442
0.7111 Intermediate Similarity NPC155873
0.7108 Intermediate Similarity NPC16349
0.7108 Intermediate Similarity NPC329914
0.7108 Intermediate Similarity NPC222244
0.7097 Intermediate Similarity NPC144133
0.7097 Intermediate Similarity NPC3952
0.7097 Intermediate Similarity NPC179394
0.7097 Intermediate Similarity NPC118078
0.7093 Intermediate Similarity NPC248775
0.7093 Intermediate Similarity NPC475699
0.7083 Intermediate Similarity NPC311166
0.7083 Intermediate Similarity NPC288350
0.7083 Intermediate Similarity NPC173329
0.7079 Intermediate Similarity NPC474809
0.7073 Intermediate Similarity NPC469660
0.7071 Intermediate Similarity NPC201191
0.7071 Intermediate Similarity NPC471993
0.7071 Intermediate Similarity NPC150463
0.7065 Intermediate Similarity NPC106332
0.7059 Intermediate Similarity NPC469880
0.7059 Intermediate Similarity NPC470024
0.7059 Intermediate Similarity NPC477202
0.7059 Intermediate Similarity NPC224660
0.7053 Intermediate Similarity NPC304968
0.7053 Intermediate Similarity NPC474338
0.7053 Intermediate Similarity NPC128488
0.7053 Intermediate Similarity NPC469491
0.7048 Intermediate Similarity NPC287075
0.7045 Intermediate Similarity NPC315731
0.7041 Intermediate Similarity NPC473204
0.7041 Intermediate Similarity NPC472187
0.7041 Intermediate Similarity NPC470761
0.7041 Intermediate Similarity NPC473219
0.7041 Intermediate Similarity NPC79631
0.7041 Intermediate Similarity NPC473545
0.7037 Intermediate Similarity NPC475760
0.7033 Intermediate Similarity NPC50637
0.7033 Intermediate Similarity NPC471480
0.703 Intermediate Similarity NPC172867
0.703 Intermediate Similarity NPC218158
0.7024 Intermediate Similarity NPC474758
0.7021 Intermediate Similarity NPC206679
0.7021 Intermediate Similarity NPC476084
0.7021 Intermediate Similarity NPC114172
0.7021 Intermediate Similarity NPC476075
0.7021 Intermediate Similarity NPC473944
0.7021 Intermediate Similarity NPC471324
0.7011 Intermediate Similarity NPC226226
0.7011 Intermediate Similarity NPC470149
0.7011 Intermediate Similarity NPC55304
0.7011 Intermediate Similarity NPC470148
0.7011 Intermediate Similarity NPC180725
0.701 Intermediate Similarity NPC96597
0.701 Intermediate Similarity NPC239547
0.701 Intermediate Similarity NPC125551
0.701 Intermediate Similarity NPC91197
0.701 Intermediate Similarity NPC309503
0.701 Intermediate Similarity NPC155319
0.701 Intermediate Similarity NPC98112
0.701 Intermediate Similarity NPC91695
0.701 Intermediate Similarity NPC70145
0.7 Intermediate Similarity NPC120009
0.7 Intermediate Similarity NPC78673
0.7 Intermediate Similarity NPC163615
0.7 Intermediate Similarity NPC472747
0.7 Intermediate Similarity NPC160517
0.7 Intermediate Similarity NPC472750
0.7 Intermediate Similarity NPC186155
0.7 Intermediate Similarity NPC197736
0.7 Intermediate Similarity NPC38569
0.7 Intermediate Similarity NPC473308
0.7 Intermediate Similarity NPC471301
0.7 Intermediate Similarity NPC473070
0.6989 Remote Similarity NPC166919
0.6989 Remote Similarity NPC64913
0.6989 Remote Similarity NPC242877
0.6979 Remote Similarity NPC281134
0.6977 Remote Similarity NPC233071
0.6977 Remote Similarity NPC474026
0.697 Remote Similarity NPC198992
0.697 Remote Similarity NPC280991
0.6966 Remote Similarity NPC471298
0.6966 Remote Similarity NPC251026
0.6947 Remote Similarity NPC159092
0.6947 Remote Similarity NPC320089
0.6947 Remote Similarity NPC109406
0.6939 Remote Similarity NPC308567
0.6939 Remote Similarity NPC187761
0.6939 Remote Similarity NPC255592
0.6939 Remote Similarity NPC261377
0.6939 Remote Similarity NPC83895
0.6932 Remote Similarity NPC133226
0.6932 Remote Similarity NPC470147
0.6932 Remote Similarity NPC474739
0.6931 Remote Similarity NPC473068
0.6931 Remote Similarity NPC169843
0.6931 Remote Similarity NPC472748
0.6923 Remote Similarity NPC215364
0.6923 Remote Similarity NPC475034
0.6923 Remote Similarity NPC316708
0.6923 Remote Similarity NPC163606
0.6915 Remote Similarity NPC80875
0.6915 Remote Similarity NPC475855
0.6915 Remote Similarity NPC62815
0.6915 Remote Similarity NPC475748
0.6915 Remote Similarity NPC473311
0.6915 Remote Similarity NPC473448
0.6907 Remote Similarity NPC73858
0.6907 Remote Similarity NPC209297
0.6907 Remote Similarity NPC194132
0.6907 Remote Similarity NPC94905
0.6907 Remote Similarity NPC475380
0.6907 Remote Similarity NPC143446
0.6907 Remote Similarity NPC8954
0.6905 Remote Similarity NPC329890
0.6905 Remote Similarity NPC476489
0.6905 Remote Similarity NPC476490
0.69 Remote Similarity NPC238397
0.69 Remote Similarity NPC471363
0.6897 Remote Similarity NPC23187

  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 NPC471552 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
0.7292 Intermediate Similarity NPD8029 Clinical (unspecified phase)
0.6875 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6813 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6739 Remote Similarity NPD1694 Approved
0.6737 Remote Similarity NPD7838 Discovery
0.6737 Remote Similarity NPD46 Approved
0.6737 Remote Similarity NPD6698 Approved
0.6731 Remote Similarity NPD6686 Approved
0.6542 Remote Similarity NPD8413 Clinical (unspecified phase)
0.6535 Remote Similarity NPD6648 Approved
0.6471 Remote Similarity NPD5344 Discontinued
0.646 Remote Similarity NPD7503 Approved
0.6383 Remote Similarity NPD1733 Clinical (unspecified phase)
0.6289 Remote Similarity NPD1695 Approved
0.625 Remote Similarity NPD4250 Approved
0.625 Remote Similarity NPD4251 Approved
0.6237 Remote Similarity NPD4752 Clinical (unspecified phase)
0.6237 Remote Similarity NPD5209 Approved
0.6195 Remote Similarity NPD7328 Approved
0.6195 Remote Similarity NPD7327 Approved
0.618 Remote Similarity NPD8039 Approved
0.6174 Remote Similarity NPD8513 Phase 3
0.6174 Remote Similarity NPD8516 Approved
0.6174 Remote Similarity NPD8517 Approved
0.6174 Remote Similarity NPD8515 Approved
0.6168 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6146 Remote Similarity NPD4249 Approved
0.6145 Remote Similarity NPD5325 Clinical (unspecified phase)
0.614 Remote Similarity NPD7516 Approved
0.6122 Remote Similarity NPD6051 Approved
0.6117 Remote Similarity NPD7638 Approved
0.6087 Remote Similarity NPD8294 Approved
0.6087 Remote Similarity NPD8377 Approved
0.6075 Remote Similarity NPD4211 Phase 1
0.6068 Remote Similarity NPD7642 Approved
0.6061 Remote Similarity NPD5785 Approved
0.6058 Remote Similarity NPD7639 Approved
0.6058 Remote Similarity NPD7640 Approved
0.604 Remote Similarity NPD5282 Discontinued
0.6036 Remote Similarity NPD6053 Discontinued
0.6034 Remote Similarity NPD8378 Approved
0.6034 Remote Similarity NPD8033 Approved
0.6034 Remote Similarity NPD8296 Approved
0.6034 Remote Similarity NPD8380 Approved
0.6034 Remote Similarity NPD8335 Approved
0.6034 Remote Similarity NPD8379 Approved
0.6022 Remote Similarity NPD4822 Approved
0.6022 Remote Similarity NPD4821 Approved
0.6022 Remote Similarity NPD4820 Approved
0.6022 Remote Similarity NPD5790 Clinical (unspecified phase)
0.6022 Remote Similarity NPD4819 Approved
0.6019 Remote Similarity NPD6412 Phase 2
0.6 Remote Similarity NPD6371 Approved
0.598 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5962 Remote Similarity NPD4225 Approved
0.5941 Remote Similarity NPD5778 Approved
0.5941 Remote Similarity NPD5779 Approved
0.5932 Remote Similarity NPD7829 Approved
0.5932 Remote Similarity NPD7830 Approved
0.5922 Remote Similarity NPD7839 Suspended
0.5917 Remote Similarity NPD8074 Phase 3
0.5895 Remote Similarity NPD6435 Approved
0.5893 Remote Similarity NPD6882 Approved
0.5882 Remote Similarity NPD7492 Approved
0.5876 Remote Similarity NPD5363 Approved
0.5876 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5872 Remote Similarity NPD5954 Clinical (unspecified phase)
0.5842 Remote Similarity NPD7637 Suspended
0.5842 Remote Similarity NPD7983 Approved
0.5833 Remote Similarity NPD7507 Approved
0.5833 Remote Similarity NPD6616 Approved
0.5833 Remote Similarity NPD7154 Phase 3
0.5816 Remote Similarity NPD6684 Approved
0.5816 Remote Similarity NPD7334 Approved
0.5816 Remote Similarity NPD7146 Approved
0.5816 Remote Similarity NPD5330 Approved
0.5816 Remote Similarity NPD7521 Approved
0.5816 Remote Similarity NPD6409 Approved
0.5812 Remote Similarity NPD6054 Approved
0.5806 Remote Similarity NPD4271 Approved
0.5806 Remote Similarity NPD4268 Approved
0.5785 Remote Similarity NPD7078 Approved
0.578 Remote Similarity NPD6008 Approved
0.5766 Remote Similarity NPD4061 Clinical (unspecified phase)
0.5748 Remote Similarity NPD7966 Clinical (unspecified phase)
0.5738 Remote Similarity NPD7736 Approved
0.5714 Remote Similarity NPD6370 Approved
0.5714 Remote Similarity NPD5955 Clinical (unspecified phase)
0.57 Remote Similarity NPD5737 Approved
0.57 Remote Similarity NPD6672 Approved
0.57 Remote Similarity NPD7513 Clinical (unspecified phase)
0.57 Remote Similarity NPD6903 Approved
0.5691 Remote Similarity NPD7319 Approved
0.569 Remote Similarity NPD7115 Discovery
0.569 Remote Similarity NPD6009 Approved
0.5686 Remote Similarity NPD5693 Phase 1
0.5684 Remote Similarity NPD5368 Approved
0.5676 Remote Similarity NPD6881 Approved
0.5676 Remote Similarity NPD6899 Approved
0.5648 Remote Similarity NPD7632 Discontinued
0.5644 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5644 Remote Similarity NPD6101 Approved
0.5641 Remote Similarity NPD7641 Discontinued
0.5638 Remote Similarity NPD5784 Clinical (unspecified phase)
0.563 Remote Similarity NPD8444 Approved
0.563 Remote Similarity NPD6015 Approved
0.563 Remote Similarity NPD6016 Approved
0.5625 Remote Similarity NPD5369 Approved
0.5612 Remote Similarity NPD7338 Clinical (unspecified phase)
0.56 Remote Similarity NPD3573 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