Structure

Physi-Chem Properties

Molecular Weight:  260.18
Volume:  298.43
LogP:  5.097
LogD:  4.208
LogS:  -4.686
# Rotatable Bonds:  9
TPSA:  33.37
# H-Bond Aceptor:  2
# H-Bond Donor:  1
# Rings:  1
# Heavy Atoms:  2

MedChem Properties

QED Drug-Likeness Score:  0.497
Synthetic Accessibility Score:  2.919
Fsp3:  0.529
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:  -4.735
MDCK Permeability:  1.935670297825709e-05
Pgp-inhibitor:  0.0
Pgp-substrate:  0.0
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.053
30% Bioavailability (F30%):  0.593

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.286
Plasma Protein Binding (PPB):  97.94779205322266%
Volume Distribution (VD):  2.552
Pgp-substrate:  0.9595488905906677%

ADMET: Metabolism

CYP1A2-inhibitor:  0.963
CYP1A2-substrate:  0.714
CYP2C19-inhibitor:  0.876
CYP2C19-substrate:  0.483
CYP2C9-inhibitor:  0.779
CYP2C9-substrate:  0.976
CYP2D6-inhibitor:  0.718
CYP2D6-substrate:  0.781
CYP3A4-inhibitor:  0.549
CYP3A4-substrate:  0.15

ADMET: Excretion

Clearance (CL):  2.943
Half-life (T1/2):  0.337

ADMET: Toxicity

hERG Blockers:  0.017
Human Hepatotoxicity (H-HT):  0.216
Drug-inuced Liver Injury (DILI):  0.427
AMES Toxicity:  0.109
Rat Oral Acute Toxicity:  0.13
Maximum Recommended Daily Dose:  0.602
Skin Sensitization:  0.915
Carcinogencity:  0.69
Eye Corrosion:  0.232
Eye Irritation:  0.841
Respiratory Toxicity:  0.934

Download Data

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

  Natural Product: NPC225272

Natural Product ID:  NPC225272
Common Name*:   Hamabiwalactone A
IUPAC Name:   (2S)-4-[(E)-dodec-1-en-11-ynyl]-2-methyl-2H-furan-5-one
Synonyms:  
Standard InCHIKey:  UDSHKXBGZYFEIY-LHNRBYRGSA-N
Standard InCHI:  InChI=1S/C17H24O2/c1-3-4-5-6-7-8-9-10-11-12-13-16-14-15(2)19-17(16)18/h1,12-15H,4-11H2,2H3/b13-12+/t15-/m0/s1
SMILES:  C#CCCCCCCCC/C=C/C1=C[C@@H](OC1=O)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL452992
PubChem CID:   44566940
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001983] Dihydrofurans
        • [CHEMONTID:0001982] Furanones
          • [CHEMONTID:0002223] Butenolides

*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
NPO19825 Litsea japonica Species Lauraceae Eukaryota leaves n.a. n.a. PMID[14575444]
NPO23895 Machilus wangchiana Species Lauraceae Eukaryota bark n.a. n.a. PMID[19916529]
NPO23895 Machilus wangchiana Species Lauraceae Eukaryota n.a. n.a. n.a. Database[UNPD]
NPO19825 Litsea japonica Species Lauraceae 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
NPT2 Others Unspecified IC50 = 714000.0 nM PMID[501170]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. Inhibition = 60.0 % PMID[501171]

☑ 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 NPC225272 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
0.9355 High Similarity NPC44343
0.9355 High Similarity NPC210303
0.9355 High Similarity NPC179087
0.8485 Intermediate Similarity NPC182794
0.8286 Intermediate Similarity NPC186531
0.8226 Intermediate Similarity NPC478117
0.8209 Intermediate Similarity NPC133904
0.8116 Intermediate Similarity NPC474823
0.8065 Intermediate Similarity NPC269615
0.8 Intermediate Similarity NPC475004
0.8 Intermediate Similarity NPC286189
0.7969 Intermediate Similarity NPC471277
0.7969 Intermediate Similarity NPC471279
0.791 Intermediate Similarity NPC473737
0.7857 Intermediate Similarity NPC218477
0.7826 Intermediate Similarity NPC248125
0.7778 Intermediate Similarity NPC478120
0.7761 Intermediate Similarity NPC151648
0.7742 Intermediate Similarity NPC106531
0.7656 Intermediate Similarity NPC474913
0.7612 Intermediate Similarity NPC471278
0.7538 Intermediate Similarity NPC245002
0.7467 Intermediate Similarity NPC329826
0.7467 Intermediate Similarity NPC469414
0.7465 Intermediate Similarity NPC21998
0.7465 Intermediate Similarity NPC203335
0.7463 Intermediate Similarity NPC22897
0.7463 Intermediate Similarity NPC159650
0.7463 Intermediate Similarity NPC474267
0.7463 Intermediate Similarity NPC222852
0.7432 Intermediate Similarity NPC474705
0.7429 Intermediate Similarity NPC131174
0.7424 Intermediate Similarity NPC212730
0.7424 Intermediate Similarity NPC265551
0.7419 Intermediate Similarity NPC236338
0.7419 Intermediate Similarity NPC15789
0.7368 Intermediate Similarity NPC4509
0.7361 Intermediate Similarity NPC470256
0.7361 Intermediate Similarity NPC276290
0.7353 Intermediate Similarity NPC130953
0.7353 Intermediate Similarity NPC299730
0.7342 Intermediate Similarity NPC150502
0.7324 Intermediate Similarity NPC191233
0.7297 Intermediate Similarity NPC84038
0.726 Intermediate Similarity NPC470693
0.7231 Intermediate Similarity NPC151761
0.7231 Intermediate Similarity NPC159535
0.7222 Intermediate Similarity NPC194871
0.7222 Intermediate Similarity NPC472266
0.7206 Intermediate Similarity NPC133600
0.7183 Intermediate Similarity NPC470688
0.7183 Intermediate Similarity NPC220766
0.7164 Intermediate Similarity NPC44542
0.7162 Intermediate Similarity NPC469660
0.7105 Intermediate Similarity NPC470686
0.7101 Intermediate Similarity NPC98519
0.7101 Intermediate Similarity NPC26223
0.7083 Intermediate Similarity NPC146811
0.7083 Intermediate Similarity NPC37382
0.7067 Intermediate Similarity NPC316185
0.7059 Intermediate Similarity NPC254095
0.7059 Intermediate Similarity NPC474084
0.7059 Intermediate Similarity NPC189700
0.7037 Intermediate Similarity NPC94200
0.7027 Intermediate Similarity NPC232812
0.7027 Intermediate Similarity NPC151481
0.7027 Intermediate Similarity NPC265574
0.7013 Intermediate Similarity NPC260396
0.6974 Remote Similarity NPC329914
0.6974 Remote Similarity NPC16349
0.6974 Remote Similarity NPC222244
0.6974 Remote Similarity NPC329890
0.6974 Remote Similarity NPC287878
0.6962 Remote Similarity NPC473471
0.6957 Remote Similarity NPC82465
0.6951 Remote Similarity NPC118423
0.6944 Remote Similarity NPC471556
0.6944 Remote Similarity NPC282760
0.6935 Remote Similarity NPC128280
0.6935 Remote Similarity NPC197467
0.6933 Remote Similarity NPC64234
0.6933 Remote Similarity NPC37929
0.6933 Remote Similarity NPC59558
0.6933 Remote Similarity NPC476012
0.6933 Remote Similarity NPC476037
0.6923 Remote Similarity NPC301207
0.6923 Remote Similarity NPC123360
0.6923 Remote Similarity NPC209113
0.6923 Remote Similarity NPC127118
0.6914 Remote Similarity NPC42470
0.6912 Remote Similarity NPC249850
0.6912 Remote Similarity NPC294938
0.6912 Remote Similarity NPC472445
0.6912 Remote Similarity NPC129150
0.6912 Remote Similarity NPC293437
0.6912 Remote Similarity NPC135863
0.6901 Remote Similarity NPC132243
0.6901 Remote Similarity NPC68110
0.6901 Remote Similarity NPC155849
0.6901 Remote Similarity NPC217940
0.6892 Remote Similarity NPC475760
0.6883 Remote Similarity NPC474758
0.6883 Remote Similarity NPC117746
0.6883 Remote Similarity NPC315843
0.6883 Remote Similarity NPC476355
0.6883 Remote Similarity NPC294434
0.6883 Remote Similarity NPC107654
0.6883 Remote Similarity NPC15499
0.6883 Remote Similarity NPC259599
0.6875 Remote Similarity NPC275316
0.6875 Remote Similarity NPC264227
0.6875 Remote Similarity NPC472965
0.6875 Remote Similarity NPC63649
0.6866 Remote Similarity NPC146551
0.6866 Remote Similarity NPC471239
0.6866 Remote Similarity NPC470963
0.6866 Remote Similarity NPC474513
0.6857 Remote Similarity NPC79756
0.6857 Remote Similarity NPC309408
0.6842 Remote Similarity NPC257618
0.6842 Remote Similarity NPC293114
0.6842 Remote Similarity NPC163003
0.6835 Remote Similarity NPC474818
0.6835 Remote Similarity NPC51809
0.6835 Remote Similarity NPC68156
0.6835 Remote Similarity NPC176329
0.6835 Remote Similarity NPC125365
0.6835 Remote Similarity NPC49302
0.6829 Remote Similarity NPC268122
0.6829 Remote Similarity NPC16321
0.6812 Remote Similarity NPC223679
0.6812 Remote Similarity NPC21946
0.6806 Remote Similarity NPC477456
0.6806 Remote Similarity NPC308457
0.6806 Remote Similarity NPC226066
0.6806 Remote Similarity NPC477457
0.6806 Remote Similarity NPC148233
0.6806 Remote Similarity NPC25747
0.68 Remote Similarity NPC476591
0.68 Remote Similarity NPC88877
0.68 Remote Similarity NPC236208
0.6795 Remote Similarity NPC478191
0.6795 Remote Similarity NPC478193
0.6795 Remote Similarity NPC329852
0.6795 Remote Similarity NPC478196
0.6795 Remote Similarity NPC478195
0.6795 Remote Similarity NPC478192
0.6795 Remote Similarity NPC478194
0.679 Remote Similarity NPC268827
0.6774 Remote Similarity NPC47946
0.6774 Remote Similarity NPC270706
0.6774 Remote Similarity NPC26600
0.6765 Remote Similarity NPC96663
0.6765 Remote Similarity NPC221763
0.6765 Remote Similarity NPC470964
0.6765 Remote Similarity NPC150717
0.6765 Remote Similarity NPC311648
0.6761 Remote Similarity NPC325929
0.6761 Remote Similarity NPC271282
0.6761 Remote Similarity NPC66460
0.6761 Remote Similarity NPC26810
0.6753 Remote Similarity NPC284006
0.675 Remote Similarity NPC128276
0.675 Remote Similarity NPC279214
0.675 Remote Similarity NPC221095
0.675 Remote Similarity NPC182292
0.675 Remote Similarity NPC184737
0.6747 Remote Similarity NPC16488
0.6719 Remote Similarity NPC135698
0.6719 Remote Similarity NPC82446
0.6714 Remote Similarity NPC478095
0.6712 Remote Similarity NPC476589
0.6712 Remote Similarity NPC273600
0.6712 Remote Similarity NPC471566
0.6712 Remote Similarity NPC471565
0.6709 Remote Similarity NPC27205
0.6709 Remote Similarity NPC188860
0.6707 Remote Similarity NPC325031
0.6707 Remote Similarity NPC471325
0.6706 Remote Similarity NPC168248
0.6667 Remote Similarity NPC474723
0.6667 Remote Similarity NPC474774
0.6667 Remote Similarity NPC471299
0.6667 Remote Similarity NPC2328
0.6667 Remote Similarity NPC191643
0.6667 Remote Similarity NPC477117
0.6667 Remote Similarity NPC140287
0.6667 Remote Similarity NPC474729
0.6667 Remote Similarity NPC178277
0.6667 Remote Similarity NPC48968
0.6667 Remote Similarity NPC29697
0.6667 Remote Similarity NPC474658
0.6667 Remote Similarity NPC287705
0.6667 Remote Similarity NPC594
0.6627 Remote Similarity NPC173609
0.6625 Remote Similarity NPC10572
0.6625 Remote Similarity NPC471225
0.6625 Remote Similarity NPC475711
0.6625 Remote Similarity NPC473825
0.6625 Remote Similarity NPC262747

  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 NPC225272 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
0.6944 Remote Similarity NPD2685 Clinical (unspecified phase)
0.6829 Remote Similarity NPD5209 Approved
0.6806 Remote Similarity NPD5325 Clinical (unspecified phase)
0.6769 Remote Similarity NPD6927 Phase 3
0.6462 Remote Similarity NPD4220 Pre-registration
0.6222 Remote Similarity NPD7838 Discovery
0.6173 Remote Similarity NPD8039 Approved
0.6164 Remote Similarity NPD4246 Clinical (unspecified phase)
0.6092 Remote Similarity NPD6400 Clinical (unspecified phase)
0.6081 Remote Similarity NPD4191 Approved
0.6081 Remote Similarity NPD4194 Approved
0.6081 Remote Similarity NPD4192 Approved
0.6081 Remote Similarity NPD4193 Approved
0.6047 Remote Similarity NPD4752 Clinical (unspecified phase)
0.6024 Remote Similarity NPD4756 Discovery
0.6023 Remote Similarity NPD6082 Clinical (unspecified phase)
0.5846 Remote Similarity NPD6096 Approved
0.5846 Remote Similarity NPD6097 Approved
0.5843 Remote Similarity NPD1694 Approved
0.5821 Remote Similarity NPD5343 Approved
0.5795 Remote Similarity NPD5332 Approved
0.5795 Remote Similarity NPD5331 Approved
0.5773 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5761 Remote Similarity NPD6051 Approved
0.5699 Remote Similarity NPD5785 Approved
0.5696 Remote Similarity NPD4247 Clinical (unspecified phase)
0.5694 Remote Similarity NPD4627 Clinical (unspecified phase)
0.5667 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5632 Remote Similarity NPD5790 Clinical (unspecified phase)
0.5618 Remote Similarity NPD7154 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