Structure

Physi-Chem Properties

Molecular Weight:  624.5
Volume:  681.734
LogP:  9.578
LogD:  4.877
LogS:  -6.805
# Rotatable Bonds:  25
TPSA:  105.45
# H-Bond Aceptor:  7
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  7

MedChem Properties

QED Drug-Likeness Score:  0.07
Synthetic Accessibility Score:  4.743
Fsp3:  0.973
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  1
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.162
MDCK Permeability:  4.191677817289019e-06
Pgp-inhibitor:  0.007
Pgp-substrate:  0.92
Human Intestinal Absorption (HIA):  0.014
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  0.866

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.003
Plasma Protein Binding (PPB):  97.1613998413086%
Volume Distribution (VD):  1.139
Pgp-substrate:  2.8384134769439697%

ADMET: Metabolism

CYP1A2-inhibitor:  0.022
CYP1A2-substrate:  0.199
CYP2C19-inhibitor:  0.072
CYP2C19-substrate:  0.06
CYP2C9-inhibitor:  0.059
CYP2C9-substrate:  0.958
CYP2D6-inhibitor:  0.011
CYP2D6-substrate:  0.047
CYP3A4-inhibitor:  0.249
CYP3A4-substrate:  0.025

ADMET: Excretion

Clearance (CL):  2.68
Half-life (T1/2):  0.021

ADMET: Toxicity

hERG Blockers:  0.962
Human Hepatotoxicity (H-HT):  0.219
Drug-inuced Liver Injury (DILI):  0.812
AMES Toxicity:  0.018
Rat Oral Acute Toxicity:  0.239
Maximum Recommended Daily Dose:  0.079
Skin Sensitization:  0.976
Carcinogencity:  0.043
Eye Corrosion:  0.003
Eye Irritation:  0.046
Respiratory Toxicity:  0.682

Download Data

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

  Natural Product: NPC228411

Natural Product ID:  NPC228411
Common Name*:   Laherradurin
IUPAC Name:   (4R,5S)-4-hydroxy-3-[(13R)-13-hydroxy-13-[(2R,5R)-5-[(2R,5R)-5-[(1S)-1-hydroxyundecyl]oxolan-2-yl]oxolan-2-yl]tridecyl]-5-methyloxolan-2-one
Synonyms:   Laherradurin
Standard InCHIKey:  FTTBSOBXDJECAA-SLOXALGKSA-N
Standard InCHI:  InChI=1S/C37H68O7/c1-3-4-5-6-7-13-16-19-22-30(38)32-24-26-34(43-32)35-27-25-33(44-35)31(39)23-20-17-14-11-9-8-10-12-15-18-21-29-36(40)28(2)42-37(29)41/h28-36,38-40H,3-27H2,1-2H3/t28-,29?,30-,31+,32+,33+,34+,35+,36-/m0/s1
SMILES:  CCCCCCCCCC[C@@H]([C@H]1CC[C@@H](O1)[C@H]1CC[C@@H](O1)[C@@H](CCCCCCCCCCCCC1C(=O)O[C@H]([C@@H]1O)C)O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL160640
PubChem CID:   44374350
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000012] Lipids and lipid-like molecules
      • [CHEMONTID:0003909] Fatty Acyls
        • [CHEMONTID:0001334] Fatty alcohols
          • [CHEMONTID:0002518] Annonaceous acetogenins

*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
NPO26361 Annona cherimolia Species Annonaceae Eukaryota Seeds n.a. n.a. PMID[11325235]
NPO26361 Annona cherimolia Species Annonaceae Eukaryota Seeds n.a. n.a. PMID[14575439]
NPO26361 Annona cherimolia Species Annonaceae Eukaryota n.a. n.a. n.a. Database[HerDing]
NPO26361 Annona cherimolia Species Annonaceae Eukaryota n.a. n.a. n.a. Database[TCMID]
NPO26361 Annona cherimolia Species Annonaceae 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
NPT5098 Protein Complex Mitochondrial complex I; NADH oxidoreductase Bos taurus IC50 = 0.18 nM PMID[572591]
NPT875 Organism Bos taurus Bos taurus IC50 = 0.29 nM PMID[572591]
NPT875 Organism Bos taurus Bos taurus Ratio = 1.6 n.a. PMID[572591]
NPT2 Others Unspecified Relative potency = 1.0 n.a. PMID[572591]
NPT2 Others Unspecified IC50 = 0.18 nM PMID[572592]

☑ 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 NPC228411 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
0.88 High Similarity NPC475616
0.863 High Similarity NPC475232
0.863 High Similarity NPC51249
0.863 High Similarity NPC473775
0.863 High Similarity NPC474100
0.863 High Similarity NPC475260
0.863 High Similarity NPC473699
0.8451 Intermediate Similarity NPC469925
0.8293 Intermediate Similarity NPC314364
0.8293 Intermediate Similarity NPC51662
0.8286 Intermediate Similarity NPC314103
0.8148 Intermediate Similarity NPC473791
0.8082 Intermediate Similarity NPC82315
0.8026 Intermediate Similarity NPC125164
0.7971 Intermediate Similarity NPC470363
0.7945 Intermediate Similarity NPC286842
0.7808 Intermediate Similarity NPC315525
0.7808 Intermediate Similarity NPC135043
0.7733 Intermediate Similarity NPC28526
0.7722 Intermediate Similarity NPC474003
0.7619 Intermediate Similarity NPC478111
0.7558 Intermediate Similarity NPC471221
0.7436 Intermediate Similarity NPC308096
0.7436 Intermediate Similarity NPC291228
0.7432 Intermediate Similarity NPC469926
0.7412 Intermediate Similarity NPC475206
0.7407 Intermediate Similarity NPC470014
0.7407 Intermediate Similarity NPC218817
0.7407 Intermediate Similarity NPC11796
0.7391 Intermediate Similarity NPC274695
0.7368 Intermediate Similarity NPC319007
0.7308 Intermediate Similarity NPC185419
0.7308 Intermediate Similarity NPC184550
0.7303 Intermediate Similarity NPC469627
0.7262 Intermediate Similarity NPC212340
0.7262 Intermediate Similarity NPC100366
0.7262 Intermediate Similarity NPC242771
0.7262 Intermediate Similarity NPC311642
0.7262 Intermediate Similarity NPC164289
0.726 Intermediate Similarity NPC469923
0.725 Intermediate Similarity NPC217725
0.7246 Intermediate Similarity NPC320588
0.7246 Intermediate Similarity NPC53463
0.7246 Intermediate Similarity NPC469937
0.7246 Intermediate Similarity NPC23155
0.72 Intermediate Similarity NPC476330
0.7191 Intermediate Similarity NPC478003
0.7191 Intermediate Similarity NPC470114
0.7191 Intermediate Similarity NPC478004
0.7191 Intermediate Similarity NPC158388
0.7179 Intermediate Similarity NPC470268
0.7176 Intermediate Similarity NPC157328
0.7159 Intermediate Similarity NPC470009
0.7159 Intermediate Similarity NPC476435
0.7159 Intermediate Similarity NPC58219
0.7159 Intermediate Similarity NPC177629
0.7126 Intermediate Similarity NPC476717
0.7125 Intermediate Similarity NPC477867
0.7125 Intermediate Similarity NPC138273
0.7093 Intermediate Similarity NPC65133
0.7079 Intermediate Similarity NPC92974
0.7067 Intermediate Similarity NPC476702
0.7045 Intermediate Similarity NPC186148
0.7037 Intermediate Similarity NPC179922
0.7033 Intermediate Similarity NPC475788
0.7027 Intermediate Similarity NPC469922
0.7011 Intermediate Similarity NPC476715
0.7 Intermediate Similarity NPC206614
0.7 Intermediate Similarity NPC474323
0.7 Intermediate Similarity NPC65359
0.6989 Remote Similarity NPC116683
0.6988 Remote Similarity NPC252483
0.6988 Remote Similarity NPC191345
0.6974 Remote Similarity NPC295256
0.6966 Remote Similarity NPC476708
0.6951 Remote Similarity NPC474020
0.6941 Remote Similarity NPC238056
0.6941 Remote Similarity NPC269318
0.6941 Remote Similarity NPC475327
0.6941 Remote Similarity NPC173328
0.6941 Remote Similarity NPC477347
0.6941 Remote Similarity NPC475270
0.6941 Remote Similarity NPC186992
0.6941 Remote Similarity NPC475667
0.6941 Remote Similarity NPC476087
0.6941 Remote Similarity NPC297768
0.6939 Remote Similarity NPC168890
0.6939 Remote Similarity NPC228311
0.6939 Remote Similarity NPC469441
0.6939 Remote Similarity NPC41674
0.6933 Remote Similarity NPC474552
0.6933 Remote Similarity NPC235788
0.6932 Remote Similarity NPC228593
0.6932 Remote Similarity NPC235196
0.6923 Remote Similarity NPC119838
0.6915 Remote Similarity NPC278028
0.6915 Remote Similarity NPC328180
0.6914 Remote Similarity NPC215030
0.6897 Remote Similarity NPC474780
0.6897 Remote Similarity NPC3464
0.6897 Remote Similarity NPC475963
0.6897 Remote Similarity NPC151176
0.6897 Remote Similarity NPC477434
0.6892 Remote Similarity NPC469921
0.6889 Remote Similarity NPC473564
0.6883 Remote Similarity NPC241949
0.6869 Remote Similarity NPC469788
0.6869 Remote Similarity NPC176756
0.6869 Remote Similarity NPC290247
0.6869 Remote Similarity NPC469787
0.6867 Remote Similarity NPC83108
0.6867 Remote Similarity NPC214030
0.686 Remote Similarity NPC148740
0.686 Remote Similarity NPC102156
0.6837 Remote Similarity NPC154962
0.6837 Remote Similarity NPC177518
0.6837 Remote Similarity NPC169089
0.6837 Remote Similarity NPC18044
0.6837 Remote Similarity NPC473701
0.6837 Remote Similarity NPC114365
0.6837 Remote Similarity NPC18433
0.6837 Remote Similarity NPC88890
0.6837 Remote Similarity NPC473526
0.6837 Remote Similarity NPC123070
0.6837 Remote Similarity NPC132304
0.6829 Remote Similarity NPC81052
0.6824 Remote Similarity NPC200446
0.6818 Remote Similarity NPC51267
0.6818 Remote Similarity NPC329749
0.6813 Remote Similarity NPC313670
0.6809 Remote Similarity NPC470883
0.6809 Remote Similarity NPC158416
0.6809 Remote Similarity NPC76862
0.6809 Remote Similarity NPC475785
0.6809 Remote Similarity NPC39859
0.68 Remote Similarity NPC167044
0.68 Remote Similarity NPC329876
0.68 Remote Similarity NPC220773
0.68 Remote Similarity NPC278693
0.6795 Remote Similarity NPC206601
0.6786 Remote Similarity NPC3852
0.6782 Remote Similarity NPC60849
0.6782 Remote Similarity NPC217559
0.6782 Remote Similarity NPC292458
0.6782 Remote Similarity NPC472352
0.6782 Remote Similarity NPC477332
0.6782 Remote Similarity NPC268578
0.6778 Remote Similarity NPC221993
0.6778 Remote Similarity NPC201046
0.6768 Remote Similarity NPC478038
0.6757 Remote Similarity NPC472019
0.6757 Remote Similarity NPC472020
0.6757 Remote Similarity NPC226602
0.6757 Remote Similarity NPC475821
0.6747 Remote Similarity NPC136424
0.6744 Remote Similarity NPC211049
0.6744 Remote Similarity NPC119922
0.6744 Remote Similarity NPC116320
0.6742 Remote Similarity NPC469626
0.6742 Remote Similarity NPC92139
0.6742 Remote Similarity NPC474949
0.6742 Remote Similarity NPC477994
0.6742 Remote Similarity NPC475491
0.6742 Remote Similarity NPC477993
0.6742 Remote Similarity NPC475019
0.6739 Remote Similarity NPC12172
0.6739 Remote Similarity NPC184463
0.6739 Remote Similarity NPC208886
0.6737 Remote Similarity NPC474313
0.6733 Remote Similarity NPC217041
0.6712 Remote Similarity NPC322148
0.6706 Remote Similarity NPC85759
0.6706 Remote Similarity NPC209995
0.6706 Remote Similarity NPC158302
0.6706 Remote Similarity NPC19841
0.6706 Remote Similarity NPC477344
0.6706 Remote Similarity NPC294748
0.6706 Remote Similarity NPC22742
0.6706 Remote Similarity NPC146992
0.6706 Remote Similarity NPC477346
0.6705 Remote Similarity NPC473299
0.6705 Remote Similarity NPC115995
0.6703 Remote Similarity NPC77001
0.6703 Remote Similarity NPC253618
0.6702 Remote Similarity NPC475900
0.6702 Remote Similarity NPC470191
0.6667 Remote Similarity NPC55678
0.6667 Remote Similarity NPC108014
0.6667 Remote Similarity NPC305182
0.6667 Remote Similarity NPC475463
0.6667 Remote Similarity NPC90904
0.6667 Remote Similarity NPC470243
0.6667 Remote Similarity NPC179746
0.6667 Remote Similarity NPC182185
0.6667 Remote Similarity NPC100078
0.6667 Remote Similarity NPC478036
0.6667 Remote Similarity NPC472021
0.6667 Remote Similarity NPC81419
0.6667 Remote Similarity NPC478037
0.6667 Remote Similarity NPC190753

  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 NPC228411 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
0.7297 Intermediate Similarity NPD7909 Approved
0.7246 Intermediate Similarity NPD3730 Approved
0.7246 Intermediate Similarity NPD3728 Approved
0.6974 Remote Similarity NPD9496 Clinical (unspecified phase)
0.6923 Remote Similarity NPD229 Approved
0.6837 Remote Similarity NPD4056 Clinical (unspecified phase)
0.6837 Remote Similarity NPD4057 Clinical (unspecified phase)
0.6786 Remote Similarity NPD4238 Approved
0.6786 Remote Similarity NPD4802 Phase 2
0.6761 Remote Similarity NPD3729 Clinical (unspecified phase)
0.6757 Remote Similarity NPD3198 Approved
0.6739 Remote Similarity NPD7983 Approved
0.6477 Remote Similarity NPD7345 Approved
0.6377 Remote Similarity NPD6125 Clinical (unspecified phase)
0.6373 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6364 Remote Similarity NPD1700 Approved
0.63 Remote Similarity NPD8085 Approved
0.63 Remote Similarity NPD8139 Approved
0.63 Remote Similarity NPD8082 Approved
0.63 Remote Similarity NPD8084 Approved
0.63 Remote Similarity NPD8086 Approved
0.63 Remote Similarity NPD8083 Approved
0.63 Remote Similarity NPD8138 Approved
0.6277 Remote Similarity NPD6698 Approved
0.6277 Remote Similarity NPD46 Approved
0.6238 Remote Similarity NPD8276 Approved
0.6238 Remote Similarity NPD8275 Approved
0.618 Remote Similarity NPD5369 Approved
0.6176 Remote Similarity NPD8081 Approved
0.6145 Remote Similarity NPD7532 Clinical (unspecified phase)
0.6133 Remote Similarity NPD73 Approved
0.6133 Remote Similarity NPD2267 Suspended
0.6117 Remote Similarity NPD8393 Approved
0.6087 Remote Similarity NPD634 Phase 3
0.6064 Remote Similarity NPD4264 Clinical (unspecified phase)
0.6053 Remote Similarity NPD8959 Approved
0.6027 Remote Similarity NPD3186 Phase 1
0.6023 Remote Similarity NPD6114 Approved
0.6023 Remote Similarity NPD6115 Approved
0.6023 Remote Similarity NPD6697 Approved
0.6023 Remote Similarity NPD6118 Approved
0.5976 Remote Similarity NPD898 Approved
0.5976 Remote Similarity NPD896 Approved
0.5976 Remote Similarity NPD897 Approved
0.5957 Remote Similarity NPD4250 Approved
0.5957 Remote Similarity NPD4251 Approved
0.5942 Remote Similarity NPD2699 Approved
0.5934 Remote Similarity NPD4270 Approved
0.5934 Remote Similarity NPD6435 Approved
0.5934 Remote Similarity NPD4269 Approved
0.5905 Remote Similarity NPD8307 Discontinued
0.5905 Remote Similarity NPD8140 Approved
0.5888 Remote Similarity NPD6371 Approved
0.587 Remote Similarity NPD7154 Phase 3
0.5867 Remote Similarity NPD615 Clinical (unspecified phase)
0.5865 Remote Similarity NPD8170 Clinical (unspecified phase)
0.5851 Remote Similarity NPD5786 Approved
0.5851 Remote Similarity NPD4249 Approved
0.5849 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5843 Remote Similarity NPD7918 Clinical (unspecified phase)
0.5843 Remote Similarity NPD7917 Clinical (unspecified phase)
0.5833 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5816 Remote Similarity NPD5779 Approved
0.5816 Remote Similarity NPD5778 Approved
0.5811 Remote Similarity NPD65 Approved
0.5811 Remote Similarity NPD9007 Approved
0.5811 Remote Similarity NPD9008 Approved
0.5811 Remote Similarity NPD9009 Approved
0.5811 Remote Similarity NPD9011 Approved
0.5811 Remote Similarity NPD8960 Approved
0.5811 Remote Similarity NPD9010 Approved
0.5811 Remote Similarity NPD64 Approved
0.5811 Remote Similarity NPD66 Approved
0.5811 Remote Similarity NPD72 Approved
0.58 Remote Similarity NPD7839 Suspended
0.5795 Remote Similarity NPD6117 Approved
0.5794 Remote Similarity NPD8306 Approved
0.5794 Remote Similarity NPD8305 Approved
0.5789 Remote Similarity NPD8269 Approved
0.5789 Remote Similarity NPD8267 Approved
0.5789 Remote Similarity NPD8268 Approved
0.5789 Remote Similarity NPD8266 Approved
0.5778 Remote Similarity NPD7329 Approved
0.5773 Remote Similarity NPD7838 Discovery
0.5758 Remote Similarity NPD5282 Discontinued
0.5747 Remote Similarity NPD6113 Clinical (unspecified phase)
0.5745 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5745 Remote Similarity NPD5363 Approved
0.5741 Remote Similarity NPD8087 Discontinued
0.573 Remote Similarity NPD6116 Phase 1
0.5714 Remote Similarity NPD4252 Approved
0.5714 Remote Similarity NPD5368 Approved
0.57 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5699 Remote Similarity NPD5362 Discontinued
0.5694 Remote Similarity NPD2266 Phase 2
0.5682 Remote Similarity NPD376 Approved
0.5682 Remote Similarity NPD11 Approved
0.5679 Remote Similarity NPD8961 Approved
0.5676 Remote Similarity NPD9638 Phase 2
0.567 Remote Similarity NPD6101 Approved
0.567 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5652 Remote Similarity NPD8517 Approved
0.5652 Remote Similarity NPD8516 Approved
0.5652 Remote Similarity NPD8513 Phase 3
0.5652 Remote Similarity NPD8515 Approved
0.5648 Remote Similarity NPD8132 Clinical (unspecified phase)
0.5632 Remote Similarity NPD3181 Approved
0.5612 Remote Similarity NPD5785 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