Structure

Physi-Chem Properties

Molecular Weight:  426.15
Volume:  415.367
LogP:  1.353
LogD:  0.908
LogS:  -2.595
# Rotatable Bonds:  13
TPSA:  131.5
# H-Bond Aceptor:  10
# H-Bond Donor:  0
# Rings:  1
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.3
Synthetic Accessibility Score:  4.718
Fsp3:  0.55
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:  -4.963
MDCK Permeability:  0.00010727564222179353
Pgp-inhibitor:  0.973
Pgp-substrate:  0.001
Human Intestinal Absorption (HIA):  0.915
20% Bioavailability (F20%):  0.088
30% Bioavailability (F30%):  0.998

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.532
Plasma Protein Binding (PPB):  21.457500457763672%
Volume Distribution (VD):  1.253
Pgp-substrate:  57.11701583862305%

ADMET: Metabolism

CYP1A2-inhibitor:  0.194
CYP1A2-substrate:  0.015
CYP2C19-inhibitor:  0.02
CYP2C19-substrate:  0.058
CYP2C9-inhibitor:  0.001
CYP2C9-substrate:  0.024
CYP2D6-inhibitor:  0.968
CYP2D6-substrate:  0.073
CYP3A4-inhibitor:  0.49
CYP3A4-substrate:  0.141

ADMET: Excretion

Clearance (CL):  2.414
Half-life (T1/2):  0.922

ADMET: Toxicity

hERG Blockers:  0.023
Human Hepatotoxicity (H-HT):  0.95
Drug-inuced Liver Injury (DILI):  0.959
AMES Toxicity:  0.895
Rat Oral Acute Toxicity:  0.356
Maximum Recommended Daily Dose:  0.026
Skin Sensitization:  0.133
Carcinogencity:  0.046
Eye Corrosion:  0.084
Eye Irritation:  0.169
Respiratory Toxicity:  0.413

Download Data

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

  Natural Product: NPC148233

Natural Product ID:  NPC148233
Common Name*:   Spicigeroide
IUPAC Name:   [(Z,2S,3S,4S,5S)-3,4,5-triacetyloxy-7-[(2R)-6-oxo-2,3-dihydropyran-2-yl]hept-6-en-2-yl] acetate
Synonyms:   spicigeroide
Standard InCHIKey:  IIGKKKGWVQSBLY-FLOMCYJLSA-N
Standard InCHI:  InChI=1S/C20H26O10/c1-11(26-12(2)21)19(28-14(4)23)20(29-15(5)24)17(27-13(3)22)10-9-16-7-6-8-18(25)30-16/h6,8-11,16-17,19-20H,7H2,1-5H3/b10-9-/t11-,16+,17-,19-,20-/m0/s1
SMILES:  C[C@@H]([C@@H]([C@H]([C@H](/C=C[C@H]1CC=CC(=O)O1)OC(=O)C)OC(=O)C)OC(=O)C)OC(=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL562047
PubChem CID:   10251859
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0002995] Pentacarboxylic acids and derivatives

*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
NPO29161 Hyptis urticoides Species Lamiaceae Eukaryota n.a. n.a. n.a. PMID[19265396]
NPO29161 Hyptis urticoides Species Lamiaceae 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
NPT1171 Cell Line HEp-2 Homo sapiens IC50 = 9.4 ug.mL-1 PMID[458367]
NPT91 Cell Line KB Homo sapiens IC50 = 5.4 ug.mL-1 PMID[458367]
NPT165 Cell Line HeLa Homo sapiens IC50 = 15.9 ug.mL-1 PMID[458367]
NPT165 Cell Line HeLa Homo sapiens Activity = 40.0 % PMID[458367]
NPT165 Cell Line HeLa Homo sapiens Activity = 34.0 % PMID[458367]
NPT165 Cell Line HeLa Homo sapiens Activity = 23.0 % PMID[458367]

☑ 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 NPC148233 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 NPC25747
0.9672 High Similarity NPC124586
0.9492 High Similarity NPC26223
0.9365 High Similarity NPC475760
0.9344 High Similarity NPC308457
0.8939 High Similarity NPC475762
0.8594 High Similarity NPC96414
0.8462 Intermediate Similarity NPC201356
0.8387 Intermediate Similarity NPC22897
0.8387 Intermediate Similarity NPC159650
0.831 Intermediate Similarity NPC474026
0.8308 Intermediate Similarity NPC19769
0.8182 Intermediate Similarity NPC276299
0.8125 Intermediate Similarity NPC26810
0.8082 Intermediate Similarity NPC473947
0.8082 Intermediate Similarity NPC180725
0.7973 Intermediate Similarity NPC470147
0.7973 Intermediate Similarity NPC133226
0.7945 Intermediate Similarity NPC248775
0.791 Intermediate Similarity NPC146811
0.7838 Intermediate Similarity NPC470148
0.7838 Intermediate Similarity NPC470149
0.7826 Intermediate Similarity NPC151481
0.7797 Intermediate Similarity NPC275316
0.7778 Intermediate Similarity NPC285840
0.7778 Intermediate Similarity NPC327041
0.7746 Intermediate Similarity NPC284006
0.7746 Intermediate Similarity NPC185186
0.7746 Intermediate Similarity NPC327383
0.7681 Intermediate Similarity NPC63873
0.7662 Intermediate Similarity NPC315559
0.7647 Intermediate Similarity NPC248125
0.7639 Intermediate Similarity NPC107654
0.7612 Intermediate Similarity NPC470808
0.7606 Intermediate Similarity NPC293114
0.7571 Intermediate Similarity NPC475982
0.7568 Intermediate Similarity NPC475711
0.7538 Intermediate Similarity NPC302564
0.7536 Intermediate Similarity NPC122627
0.7536 Intermediate Similarity NPC203335
0.7532 Intermediate Similarity NPC251026
0.7532 Intermediate Similarity NPC313677
0.75 Intermediate Similarity NPC273600
0.7465 Intermediate Similarity NPC202011
0.7465 Intermediate Similarity NPC476012
0.7465 Intermediate Similarity NPC476037
0.7463 Intermediate Similarity NPC474774
0.7436 Intermediate Similarity NPC473315
0.7436 Intermediate Similarity NPC44261
0.7436 Intermediate Similarity NPC142111
0.7424 Intermediate Similarity NPC79756
0.7403 Intermediate Similarity NPC469469
0.7397 Intermediate Similarity NPC315843
0.7391 Intermediate Similarity NPC475675
0.7391 Intermediate Similarity NPC475555
0.7368 Intermediate Similarity NPC1180
0.7361 Intermediate Similarity NPC316185
0.7344 Intermediate Similarity NPC86948
0.7344 Intermediate Similarity NPC245002
0.7342 Intermediate Similarity NPC473308
0.7324 Intermediate Similarity NPC88877
0.7324 Intermediate Similarity NPC476591
0.7313 Intermediate Similarity NPC151648
0.7313 Intermediate Similarity NPC15193
0.7286 Intermediate Similarity NPC478100
0.7273 Intermediate Similarity NPC478095
0.7273 Intermediate Similarity NPC97570
0.7273 Intermediate Similarity NPC474267
0.726 Intermediate Similarity NPC329914
0.726 Intermediate Similarity NPC329890
0.725 Intermediate Similarity NPC470124
0.7246 Intermediate Similarity NPC282760
0.7246 Intermediate Similarity NPC182794
0.7246 Intermediate Similarity NPC470123
0.7237 Intermediate Similarity NPC318481
0.7237 Intermediate Similarity NPC477314
0.7231 Intermediate Similarity NPC294938
0.7206 Intermediate Similarity NPC179087
0.7206 Intermediate Similarity NPC210303
0.7206 Intermediate Similarity NPC44343
0.7188 Intermediate Similarity NPC474913
0.7183 Intermediate Similarity NPC238223
0.7179 Intermediate Similarity NPC297440
0.716 Intermediate Similarity NPC208473
0.7143 Intermediate Similarity NPC284447
0.7143 Intermediate Similarity NPC271632
0.7143 Intermediate Similarity NPC139712
0.7143 Intermediate Similarity NPC478101
0.7121 Intermediate Similarity NPC478096
0.7105 Intermediate Similarity NPC233071
0.7101 Intermediate Similarity NPC477456
0.7101 Intermediate Similarity NPC477457
0.7067 Intermediate Similarity NPC473948
0.7042 Intermediate Similarity NPC478097
0.7042 Intermediate Similarity NPC132286
0.7042 Intermediate Similarity NPC194871
0.7037 Intermediate Similarity NPC475034
0.7031 Intermediate Similarity NPC151761
0.7031 Intermediate Similarity NPC159535
0.7027 Intermediate Similarity NPC222244
0.7027 Intermediate Similarity NPC16349
0.7024 Intermediate Similarity NPC177668
0.7015 Intermediate Similarity NPC286189
0.7013 Intermediate Similarity NPC182292
0.7 Intermediate Similarity NPC478099
0.7 Intermediate Similarity NPC478098
0.7 Intermediate Similarity NPC476589
0.6988 Remote Similarity NPC470137
0.6986 Remote Similarity NPC469660
0.6974 Remote Similarity NPC188860
0.6974 Remote Similarity NPC326661
0.697 Remote Similarity NPC471277
0.697 Remote Similarity NPC129150
0.697 Remote Similarity NPC471279
0.6957 Remote Similarity NPC217940
0.6944 Remote Similarity NPC218477
0.6944 Remote Similarity NPC470256
0.6935 Remote Similarity NPC15789
0.6935 Remote Similarity NPC236338
0.6933 Remote Similarity NPC473489
0.6933 Remote Similarity NPC474280
0.6923 Remote Similarity NPC473981
0.6923 Remote Similarity NPC473980
0.6914 Remote Similarity NPC475035
0.6914 Remote Similarity NPC266718
0.6912 Remote Similarity NPC321919
0.6912 Remote Similarity NPC81896
0.6905 Remote Similarity NPC133450
0.6901 Remote Similarity NPC37382
0.6883 Remote Similarity NPC97516
0.6883 Remote Similarity NPC474278
0.6875 Remote Similarity NPC474959
0.6875 Remote Similarity NPC11383
0.6875 Remote Similarity NPC475046
0.6875 Remote Similarity NPC475690
0.6875 Remote Similarity NPC310450
0.6867 Remote Similarity NPC475037
0.6866 Remote Similarity NPC254095
0.6866 Remote Similarity NPC474084
0.6866 Remote Similarity NPC223679
0.6857 Remote Similarity NPC114464
0.6842 Remote Similarity NPC260396
0.6842 Remote Similarity NPC473582
0.6824 Remote Similarity NPC473311
0.6824 Remote Similarity NPC3952
0.6818 Remote Similarity NPC472808
0.6818 Remote Similarity NPC324224
0.6812 Remote Similarity NPC55376
0.6806 Remote Similarity NPC25298
0.6806 Remote Similarity NPC225272
0.68 Remote Similarity NPC477303
0.68 Remote Similarity NPC477311
0.68 Remote Similarity NPC474705
0.6795 Remote Similarity NPC475699
0.6795 Remote Similarity NPC28049
0.6795 Remote Similarity NPC279532
0.6795 Remote Similarity NPC473471
0.679 Remote Similarity NPC286770
0.679 Remote Similarity NPC284472
0.679 Remote Similarity NPC229799
0.6782 Remote Similarity NPC256368
0.6769 Remote Similarity NPC478120
0.6765 Remote Similarity NPC222852
0.6765 Remote Similarity NPC82465
0.6761 Remote Similarity NPC471566
0.6761 Remote Similarity NPC471556
0.6761 Remote Similarity NPC471565
0.6757 Remote Similarity NPC473361
0.6757 Remote Similarity NPC329904
0.6757 Remote Similarity NPC59558
0.6753 Remote Similarity NPC470705
0.6753 Remote Similarity NPC49392
0.6753 Remote Similarity NPC203277
0.6753 Remote Similarity NPC301207
0.6753 Remote Similarity NPC301525
0.6753 Remote Similarity NPC190400
0.6753 Remote Similarity NPC209113
0.6753 Remote Similarity NPC127118
0.675 Remote Similarity NPC184208
0.675 Remote Similarity NPC8538
0.675 Remote Similarity NPC315731
0.6721 Remote Similarity NPC128280
0.6721 Remote Similarity NPC197467
0.6719 Remote Similarity NPC106531
0.6716 Remote Similarity NPC135863
0.6716 Remote Similarity NPC265551
0.6716 Remote Similarity NPC249850
0.6716 Remote Similarity NPC293437
0.6716 Remote Similarity NPC212730
0.6714 Remote Similarity NPC68110
0.6714 Remote Similarity NPC473737
0.6714 Remote Similarity NPC54925
0.6712 Remote Similarity NPC310210
0.6712 Remote Similarity NPC474823
0.6712 Remote Similarity NPC477117
0.6711 Remote Similarity NPC477315
0.6711 Remote Similarity NPC477309
0.6711 Remote Similarity NPC474758
0.6711 Remote Similarity NPC477304
0.6711 Remote Similarity NPC477316

  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 NPC148233 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
0.6761 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6628 Remote Similarity NPD7838 Discovery
0.6562 Remote Similarity NPD6927 Phase 3
0.6437 Remote Similarity NPD6698 Approved
0.6437 Remote Similarity NPD46 Approved
0.6377 Remote Similarity NPD9119 Approved
0.6377 Remote Similarity NPD585 Clinical (unspecified phase)
0.6377 Remote Similarity NPD69 Approved
0.6377 Remote Similarity NPD6109 Phase 1
0.6349 Remote Similarity NPD5343 Approved
0.631 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6232 Remote Similarity NPD9118 Approved
0.6129 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6129 Remote Similarity NPD6096 Approved
0.6129 Remote Similarity NPD6097 Approved
0.6071 Remote Similarity NPD5209 Approved
0.6064 Remote Similarity NPD6648 Approved
0.6 Remote Similarity NPD5344 Discontinued
0.5972 Remote Similarity NPD4246 Clinical (unspecified phase)
0.5946 Remote Similarity NPD5325 Clinical (unspecified phase)
0.5921 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5833 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5789 Remote Similarity NPD4225 Approved
0.5781 Remote Similarity NPD3174 Discontinued
0.5763 Remote Similarity NPD9115 Approved
0.5758 Remote Similarity NPD4220 Pre-registration
0.5698 Remote Similarity NPD4752 Clinical (unspecified phase)
0.5682 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5663 Remote Similarity NPD4756 Discovery
0.5652 Remote Similarity NPD7983 Approved
0.561 Remote Similarity NPD8039 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