Structure

Physi-Chem Properties

Molecular Weight:  381.17
Volume:  373.71
LogP:  3.719
LogD:  3.482
LogS:  -4.064
# Rotatable Bonds:  1
TPSA:  82.55
# H-Bond Aceptor:  5
# H-Bond Donor:  3
# Rings:  4
# Heavy Atoms:  6

MedChem Properties

QED Drug-Likeness Score:  0.634
Synthetic Accessibility Score:  5.319
Fsp3:  0.75
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.096
MDCK Permeability:  1.7899366866913624e-05
Pgp-inhibitor:  0.016
Pgp-substrate:  0.646
Human Intestinal Absorption (HIA):  0.011
20% Bioavailability (F20%):  0.007
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.821
Plasma Protein Binding (PPB):  59.321502685546875%
Volume Distribution (VD):  4.094
Pgp-substrate:  34.281471252441406%

ADMET: Metabolism

CYP1A2-inhibitor:  0.014
CYP1A2-substrate:  0.844
CYP2C19-inhibitor:  0.03
CYP2C19-substrate:  0.414
CYP2C9-inhibitor:  0.233
CYP2C9-substrate:  0.912
CYP2D6-inhibitor:  0.016
CYP2D6-substrate:  0.657
CYP3A4-inhibitor:  0.36
CYP3A4-substrate:  0.235

ADMET: Excretion

Clearance (CL):  10.701
Half-life (T1/2):  0.513

ADMET: Toxicity

hERG Blockers:  0.03
Human Hepatotoxicity (H-HT):  0.417
Drug-inuced Liver Injury (DILI):  0.668
AMES Toxicity:  0.012
Rat Oral Acute Toxicity:  0.804
Maximum Recommended Daily Dose:  0.984
Skin Sensitization:  0.27
Carcinogencity:  0.32
Eye Corrosion:  0.003
Eye Irritation:  0.018
Respiratory Toxicity:  0.959

Download Data

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

  Natural Product: NPC42590

Natural Product ID:  NPC42590
Common Name*:   Haterumaimide I
IUPAC Name:   (3R)-3-[(2S,3aS,5aS,8S,9aR,9bR)-8-chloro-3a,6,6,9a-tetramethyl-5-oxo-1,2,4,5a,7,8,9,9b-octahydrobenzo[e][1]benzofuran-2-yl]pyrrolidine-2,5-dione
Synonyms:   Haterumaimide I
Standard InCHIKey:  UJSKCGOTHYDOCV-LCIZUERQSA-N
Standard InCHI:  InChI=1S/C20H28ClNO4/c1-18(2)7-10(21)8-19(3)14-6-13(11-5-15(24)22-17(11)25)26-20(14,4)9-12(23)16(18)19/h10-11,13-14,16H,5-9H2,1-4H3,(H,22,24,25)/t10-,11+,13-,14+,16-,19+,20-/m0/s1
SMILES:  OC1=NC(=O)[C@H](C1)[C@@H]1C[C@H]2[C@](O1)(C)CC(=O)[C@@H]1[C@]2(C)C[C@@H](Cl)CC1(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL464430
PubChem CID:   11783867
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0001634] Naphthofurans

*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
NPO33282 lissoclinum sp. Species Didemnidae Eukaryota n.a. n.a. n.a. PMID[11575950]

☑ 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
NPT168 Cell Line P388 Mus musculus IC50 > 10.0 ug.mL-1 PMID[523948]
NPT27 Others Unspecified Inhibition = 80.0 % PMID[523948]

☑ 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 NPC42590 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
0.8241 Intermediate Similarity NPC168733
0.8131 Intermediate Similarity NPC259476
0.7928 Intermediate Similarity NPC92829
0.7876 Intermediate Similarity NPC122404
0.7652 Intermediate Similarity NPC24462
0.7632 Intermediate Similarity NPC7797
0.7373 Intermediate Similarity NPC216335
0.6694 Remote Similarity NPC106479
0.6583 Remote Similarity NPC46764
0.6455 Remote Similarity NPC61688
0.6449 Remote Similarity NPC477434
0.6449 Remote Similarity NPC34984
0.6449 Remote Similarity NPC25037
0.6429 Remote Similarity NPC226513
0.6364 Remote Similarity NPC477614
0.6364 Remote Similarity NPC226491
0.6346 Remote Similarity NPC200085
0.6346 Remote Similarity NPC314858
0.6346 Remote Similarity NPC253703
0.6346 Remote Similarity NPC51695
0.6346 Remote Similarity NPC475725
0.6321 Remote Similarity NPC50658
0.6306 Remote Similarity NPC67653
0.6306 Remote Similarity NPC471459
0.6306 Remote Similarity NPC200580
0.6306 Remote Similarity NPC477443
0.6306 Remote Similarity NPC477440
0.6296 Remote Similarity NPC475689
0.6286 Remote Similarity NPC275243
0.625 Remote Similarity NPC477433
0.625 Remote Similarity NPC307865
0.625 Remote Similarity NPC475056
0.625 Remote Similarity NPC477444
0.625 Remote Similarity NPC477442
0.6228 Remote Similarity NPC247877
0.6228 Remote Similarity NPC309127
0.6226 Remote Similarity NPC134227
0.6216 Remote Similarity NPC471221
0.6216 Remote Similarity NPC90676
0.6182 Remote Similarity NPC120395
0.6182 Remote Similarity NPC80700
0.6176 Remote Similarity NPC109510
0.6176 Remote Similarity NPC474755
0.6147 Remote Similarity NPC50438
0.6121 Remote Similarity NPC193785
0.6111 Remote Similarity NPC470540
0.6091 Remote Similarity NPC473350
0.6087 Remote Similarity NPC470424
0.6075 Remote Similarity NPC125366
0.6055 Remote Similarity NPC472847
0.6055 Remote Similarity NPC15091
0.6047 Remote Similarity NPC323532
0.6036 Remote Similarity NPC477441
0.6036 Remote Similarity NPC475729
0.6036 Remote Similarity NPC476717
0.6036 Remote Similarity NPC474215
0.6034 Remote Similarity NPC17336
0.6019 Remote Similarity NPC58631
0.6017 Remote Similarity NPC474952
0.6 Remote Similarity NPC472237
0.6 Remote Similarity NPC472984
0.6 Remote Similarity NPC472487
0.6 Remote Similarity NPC105895
0.6 Remote Similarity NPC237938
0.6 Remote Similarity NPC476189
0.6 Remote Similarity NPC219535
0.6 Remote Similarity NPC472486
0.6 Remote Similarity NPC65133
0.6 Remote Similarity NPC472238
0.5982 Remote Similarity NPC263802
0.5981 Remote Similarity NPC474754
0.5969 Remote Similarity NPC476956
0.5968 Remote Similarity NPC474725
0.5963 Remote Similarity NPC13494
0.5962 Remote Similarity NPC55508
0.5946 Remote Similarity NPC477445
0.5946 Remote Similarity NPC477205
0.5946 Remote Similarity NPC62572
0.5935 Remote Similarity NPC475800
0.5932 Remote Similarity NPC190080
0.5932 Remote Similarity NPC111187
0.5929 Remote Similarity NPC3032
0.5929 Remote Similarity NPC473319
0.5929 Remote Similarity NPC131104
0.5929 Remote Similarity NPC476435
0.5926 Remote Similarity NPC476957
0.5922 Remote Similarity NPC89310
0.592 Remote Similarity NPC328052
0.5917 Remote Similarity NPC178853
0.5913 Remote Similarity NPC216137
0.5913 Remote Similarity NPC475878
0.5909 Remote Similarity NPC327451
0.5909 Remote Similarity NPC292458
0.5909 Remote Similarity NPC217559
0.5909 Remote Similarity NPC268578
0.5905 Remote Similarity NPC21220
0.5905 Remote Similarity NPC159789
0.5905 Remote Similarity NPC125767
0.5902 Remote Similarity NPC88469
0.5897 Remote Similarity NPC287354
0.5897 Remote Similarity NPC62407
0.5893 Remote Similarity NPC83242
0.5893 Remote Similarity NPC248216
0.5873 Remote Similarity NPC12270
0.5872 Remote Similarity NPC48756
0.5872 Remote Similarity NPC475743
0.5872 Remote Similarity NPC280781
0.5862 Remote Similarity NPC161035
0.5856 Remote Similarity NPC473299
0.5856 Remote Similarity NPC319909
0.5856 Remote Similarity NPC473336
0.5856 Remote Similarity NPC474996
0.5856 Remote Similarity NPC471044
0.5849 Remote Similarity NPC471046
0.5849 Remote Similarity NPC474020
0.5847 Remote Similarity NPC477264
0.5847 Remote Similarity NPC116683
0.5847 Remote Similarity NPC476728
0.5833 Remote Similarity NPC267921
0.5833 Remote Similarity NPC320144
0.5826 Remote Similarity NPC88337
0.5826 Remote Similarity NPC475211
0.5826 Remote Similarity NPC185529
0.5826 Remote Similarity NPC472146
0.5818 Remote Similarity NPC289486
0.5818 Remote Similarity NPC61107
0.5818 Remote Similarity NPC317066
0.581 Remote Similarity NPC133922
0.5794 Remote Similarity NPC471151
0.5794 Remote Similarity NPC475031
0.5794 Remote Similarity NPC23884
0.5794 Remote Similarity NPC143250
0.5794 Remote Similarity NPC221420
0.5789 Remote Similarity NPC221993
0.5789 Remote Similarity NPC236459
0.578 Remote Similarity NPC1882
0.5776 Remote Similarity NPC250753
0.5772 Remote Similarity NPC13149
0.5766 Remote Similarity NPC227170
0.5766 Remote Similarity NPC269684
0.5763 Remote Similarity NPC305808
0.576 Remote Similarity NPC128210
0.5755 Remote Similarity NPC68565
0.5755 Remote Similarity NPC35871
0.5752 Remote Similarity NPC476727
0.5752 Remote Similarity NPC476726
0.5752 Remote Similarity NPC476730
0.575 Remote Similarity NPC471038
0.575 Remote Similarity NPC472144
0.575 Remote Similarity NPC253995
0.575 Remote Similarity NPC109059
0.575 Remote Similarity NPC288
0.575 Remote Similarity NPC476294
0.5743 Remote Similarity NPC84562
0.5741 Remote Similarity NPC185465
0.5739 Remote Similarity NPC253618
0.5739 Remote Similarity NPC77001
0.5738 Remote Similarity NPC471254
0.5728 Remote Similarity NPC131892
0.5728 Remote Similarity NPC213178
0.5728 Remote Similarity NPC327728
0.5728 Remote Similarity NPC6120
0.5727 Remote Similarity NPC474870
0.5727 Remote Similarity NPC254123
0.5727 Remote Similarity NPC271572
0.5726 Remote Similarity NPC474379
0.5726 Remote Similarity NPC472147
0.5726 Remote Similarity NPC59170
0.5726 Remote Similarity NPC147272
0.5726 Remote Similarity NPC472231
0.5726 Remote Similarity NPC472148
0.5726 Remote Similarity NPC472232
0.5725 Remote Similarity NPC470276
0.5714 Remote Similarity NPC13949
0.5714 Remote Similarity NPC175419
0.5714 Remote Similarity NPC181871
0.5714 Remote Similarity NPC235109
0.5714 Remote Similarity NPC9060
0.5714 Remote Similarity NPC163685
0.5714 Remote Similarity NPC165616
0.5714 Remote Similarity NPC232112
0.5714 Remote Similarity NPC475785
0.5714 Remote Similarity NPC475765
0.5714 Remote Similarity NPC79308
0.5702 Remote Similarity NPC80417
0.5702 Remote Similarity NPC470920
0.5702 Remote Similarity NPC46761
0.5702 Remote Similarity NPC239938
0.5701 Remote Similarity NPC475742
0.5701 Remote Similarity NPC5767
0.5701 Remote Similarity NPC108840
0.5693 Remote Similarity NPC477352
0.5691 Remote Similarity NPC471253
0.569 Remote Similarity NPC180849
0.569 Remote Similarity NPC470114
0.569 Remote Similarity NPC80401
0.569 Remote Similarity NPC312637
0.569 Remote Similarity NPC476296
0.5688 Remote Similarity NPC73013
0.5688 Remote Similarity NPC245029

  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 NPC42590 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
0.6016 Remote Similarity NPD6415 Discontinued
0.5966 Remote Similarity NPD8418 Phase 2
0.5905 Remote Similarity NPD3703 Phase 2
0.5887 Remote Similarity NPD6334 Approved
0.5887 Remote Similarity NPD6333 Approved
0.5873 Remote Similarity NPD5215 Approved
0.5873 Remote Similarity NPD1719 Phase 1
0.5802 Remote Similarity NPD7100 Approved
0.5736 Remote Similarity NPD5167 Approved
0.5728 Remote Similarity NPD3700 Clinical (unspecified phase)
0.5728 Remote Similarity NPD3699 Clinical (unspecified phase)
0.5727 Remote Similarity NPD1448 Clinical (unspecified phase)
0.5693 Remote Similarity NPD6033 Approved
0.5669 Remote Similarity NPD5169 Approved
0.5659 Remote Similarity NPD8298 Phase 2
0.5648 Remote Similarity NPD6116 Phase 1
0.5625 Remote Similarity NPD5127 Approved
0.5625 Remote Similarity NPD5216 Approved
0.5625 Remote Similarity NPD5217 Approved
0.5619 Remote Similarity NPD4809 Clinical (unspecified phase)
0.5619 Remote Similarity NPD4808 Clinical (unspecified phase)
0.5606 Remote Similarity NPD6314 Approved
0.5606 Remote Similarity NPD6313 Approved
0.5606 Remote Similarity NPD6335 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