Structure

Physi-Chem Properties

Molecular Weight:  1020.51
Volume:  987.673
LogP:  6.881
LogD:  4.504
LogS:  -6.618
# Rotatable Bonds:  0
TPSA:  172.59
# H-Bond Aceptor:  17
# H-Bond Donor:  0
# Rings:  16
# Heavy Atoms:  17

MedChem Properties

QED Drug-Likeness Score:  0.205
Synthetic Accessibility Score:  8.805
Fsp3:  0.893
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  0
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.052
MDCK Permeability:  0.00026559410616755486
Pgp-inhibitor:  0.0
Pgp-substrate:  0.999
Human Intestinal Absorption (HIA):  0.005
20% Bioavailability (F20%):  0.0
30% Bioavailability (F30%):  0.019

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  77.10443878173828%
Volume Distribution (VD):  0.306
Pgp-substrate:  10.630934715270996%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.788
CYP2C19-inhibitor:  0.033
CYP2C19-substrate:  0.882
CYP2C9-inhibitor:  0.08
CYP2C9-substrate:  0.0
CYP2D6-inhibitor:  0.017
CYP2D6-substrate:  0.049
CYP3A4-inhibitor:  0.983
CYP3A4-substrate:  0.898

ADMET: Excretion

Clearance (CL):  15.596
Half-life (T1/2):  0.006

ADMET: Toxicity

hERG Blockers:  0.869
Human Hepatotoxicity (H-HT):  0.88
Drug-inuced Liver Injury (DILI):  0.984
AMES Toxicity:  0.754
Rat Oral Acute Toxicity:  0.996
Maximum Recommended Daily Dose:  0.998
Skin Sensitization:  0.954
Carcinogencity:  0.086
Eye Corrosion:  0.003
Eye Irritation:  0.013
Respiratory Toxicity:  0.985

Download Data

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

  Natural Product: NPC475275

Natural Product ID:  NPC475275
Common Name*:   DUCBCVCRNZWTID-QROFZPEOSA-N
IUPAC Name:   n.a.
Synonyms:   Halichondrin B-1020
Standard InCHIKey:  DUCBCVCRNZWTID-QROFZPEOSA-N
Standard InCHI:  InChI=1S/C56H76O17/c1-24-13-30-7-9-33-25(2)14-32(59-33)11-12-54-22-41-50(72-54)51-52(65-41)53(73-54)49-34(63-51)10-8-31(61-49)15-43(57)67-48-29(6)47-38(62-37(48)16-35(60-30)28(24)5)17-36-40(64-47)21-56(68-36)23-42-46(71-56)27(4)20-55(70-42)19-26(3)45-39(69-55)18-44(58)66-45/h24,26-27,29-42,45-53H,2,5,7-23H2,1,3-4,6H3/t24-,26+,27+,29+,30+,31-,32+,33+,34+,35-,36-,37+,38+,39+,40-,41-,42+,45+,46+,47+,48-,49+,50+,51+,52-,53+,54+,55-,56+/m1/s1
SMILES:  O=C1C[C@H]2CC[C@H]3[C@H](O2)[C@@H]2O[C@]4(CC[C@@H]5O[C@@H](CC[C@@H]6O[C@H](C[C@H]7[C@H](O1)[C@@H](C)[C@H]1[C@@H](O7)C[C@@H]7[C@H](O1)C[C@]1(O7)O[C@@H]7[C@H](C1)O[C@@]1(C[C@@H]7C)C[C@H](C)[C@H]7[C@@H](O1)CC(=O)O7)C(=C)[C@@H](C6)C)C(=C)C5)O[C@@H]1[C@H](O3)[C@H]2O[C@@H]1C4
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL502614
PubChem CID:   44581726
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0001542] Disaccharides

*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
NPO32553 lissodendoryx sp. Species Coelosphaeridae Eukaryota n.a. New Zealand n.a. PMID[19081259]

☑ 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 = 0.0011 ug.mL-1 PMID[518244]

☑ 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 NPC475275 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 NPC473771
0.9429 High Similarity NPC475537
0.9429 High Similarity NPC308858
0.9423 High Similarity NPC312498
0.9423 High Similarity NPC473849
0.875 High Similarity NPC475298
0.7568 Intermediate Similarity NPC231271
0.7568 Intermediate Similarity NPC470519
0.7478 Intermediate Similarity NPC297945
0.7478 Intermediate Similarity NPC126897
0.7315 Intermediate Similarity NPC167893
0.7155 Intermediate Similarity NPC313668
0.7155 Intermediate Similarity NPC315836
0.7143 Intermediate Similarity NPC51662
0.7107 Intermediate Similarity NPC93688
0.7107 Intermediate Similarity NPC109603
0.7027 Intermediate Similarity NPC236580
0.7027 Intermediate Similarity NPC304445
0.6935 Remote Similarity NPC469812
0.6935 Remote Similarity NPC183353
0.6897 Remote Similarity NPC476740
0.6897 Remote Similarity NPC476738
0.6887 Remote Similarity NPC304558
0.687 Remote Similarity NPC475367
0.687 Remote Similarity NPC473816
0.687 Remote Similarity NPC473148
0.687 Remote Similarity NPC474581
0.686 Remote Similarity NPC54395
0.6855 Remote Similarity NPC329008
0.6855 Remote Similarity NPC317635
0.6842 Remote Similarity NPC67296
0.6842 Remote Similarity NPC162024
0.6825 Remote Similarity NPC186339
0.6822 Remote Similarity NPC314364
0.6814 Remote Similarity NPC49833
0.6814 Remote Similarity NPC249171
0.68 Remote Similarity NPC170880
0.6797 Remote Similarity NPC11732
0.6789 Remote Similarity NPC206614
0.6789 Remote Similarity NPC474323
0.6786 Remote Similarity NPC473605
0.6786 Remote Similarity NPC473765
0.6786 Remote Similarity NPC475241
0.6786 Remote Similarity NPC476066
0.6786 Remote Similarity NPC474297
0.6786 Remote Similarity NPC475593
0.6786 Remote Similarity NPC475164
0.6786 Remote Similarity NPC475525
0.6786 Remote Similarity NPC475540
0.6786 Remote Similarity NPC475375
0.6774 Remote Similarity NPC207738
0.6769 Remote Similarity NPC300655
0.6769 Remote Similarity NPC222951
0.6769 Remote Similarity NPC311178
0.6769 Remote Similarity NPC43589
0.6752 Remote Similarity NPC478038
0.6748 Remote Similarity NPC156651
0.6729 Remote Similarity NPC162071
0.6726 Remote Similarity NPC263674
0.6726 Remote Similarity NPC261372
0.6726 Remote Similarity NPC58267
0.6724 Remote Similarity NPC309398
0.672 Remote Similarity NPC108072
0.672 Remote Similarity NPC147635
0.672 Remote Similarity NPC163693
0.6718 Remote Similarity NPC183816
0.6718 Remote Similarity NPC473679
0.6718 Remote Similarity NPC322904
0.6718 Remote Similarity NPC233223
0.6718 Remote Similarity NPC475177
0.6718 Remote Similarity NPC475444
0.6718 Remote Similarity NPC324933
0.6718 Remote Similarity NPC196874
0.6718 Remote Similarity NPC319719
0.6697 Remote Similarity NPC92974
0.6695 Remote Similarity NPC287269
0.6694 Remote Similarity NPC232237
0.6694 Remote Similarity NPC105800
0.6694 Remote Similarity NPC470543
0.6693 Remote Similarity NPC256983
0.6667 Remote Similarity NPC469823
0.6667 Remote Similarity NPC51099
0.6667 Remote Similarity NPC475501
0.6667 Remote Similarity NPC474917
0.6667 Remote Similarity NPC248415
0.6667 Remote Similarity NPC275225
0.6667 Remote Similarity NPC293031
0.6667 Remote Similarity NPC469820
0.6667 Remote Similarity NPC477463
0.6667 Remote Similarity NPC68767
0.6641 Remote Similarity NPC473474
0.6641 Remote Similarity NPC469351
0.6639 Remote Similarity NPC146563
0.6639 Remote Similarity NPC193765
0.6639 Remote Similarity NPC475960
0.6639 Remote Similarity NPC224414
0.6638 Remote Similarity NPC80144
0.6638 Remote Similarity NPC313569
0.6637 Remote Similarity NPC148872
0.6635 Remote Similarity NPC474981
0.6617 Remote Similarity NPC477234
0.6615 Remote Similarity NPC45606
0.6615 Remote Similarity NPC172823
0.6615 Remote Similarity NPC220838
0.6615 Remote Similarity NPC470476
0.6613 Remote Similarity NPC473824
0.6613 Remote Similarity NPC473452
0.6613 Remote Similarity NPC102505
0.6613 Remote Similarity NPC104137
0.6613 Remote Similarity NPC69811
0.6613 Remote Similarity NPC8524
0.6613 Remote Similarity NPC286457
0.6613 Remote Similarity NPC136768
0.6613 Remote Similarity NPC475209
0.6613 Remote Similarity NPC309223
0.6613 Remote Similarity NPC471580
0.6613 Remote Similarity NPC191827
0.6613 Remote Similarity NPC475514
0.6613 Remote Similarity NPC123522
0.6613 Remote Similarity NPC470876
0.6613 Remote Similarity NPC185466
0.6613 Remote Similarity NPC110633
0.6613 Remote Similarity NPC85154
0.6613 Remote Similarity NPC220160
0.6613 Remote Similarity NPC148417
0.6613 Remote Similarity NPC33012
0.6613 Remote Similarity NPC475119
0.661 Remote Similarity NPC469401
0.661 Remote Similarity NPC315070
0.6607 Remote Similarity NPC477345
0.6607 Remote Similarity NPC477348
0.6607 Remote Similarity NPC163409
0.6607 Remote Similarity NPC44682
0.6607 Remote Similarity NPC472198
0.6607 Remote Similarity NPC238264
0.6606 Remote Similarity NPC177629
0.6606 Remote Similarity NPC58219
0.6604 Remote Similarity NPC474472
0.6604 Remote Similarity NPC472352
0.6604 Remote Similarity NPC477332
0.6604 Remote Similarity NPC257358
0.6604 Remote Similarity NPC60849
0.6589 Remote Similarity NPC273962
0.6589 Remote Similarity NPC470218
0.6587 Remote Similarity NPC476127
0.6587 Remote Similarity NPC37860
0.6587 Remote Similarity NPC473645
0.6587 Remote Similarity NPC153673
0.6587 Remote Similarity NPC142151
0.6587 Remote Similarity NPC476150
0.6587 Remote Similarity NPC110385
0.6587 Remote Similarity NPC267694
0.6587 Remote Similarity NPC268184
0.6587 Remote Similarity NPC144644
0.6585 Remote Similarity NPC469821
0.6577 Remote Similarity NPC470373
0.6577 Remote Similarity NPC470379
0.6574 Remote Similarity NPC474762
0.6574 Remote Similarity NPC476015
0.6565 Remote Similarity NPC477235
0.6562 Remote Similarity NPC160084
0.6562 Remote Similarity NPC106589
0.6562 Remote Similarity NPC202261
0.6562 Remote Similarity NPC42747
0.656 Remote Similarity NPC237191
0.656 Remote Similarity NPC36831
0.656 Remote Similarity NPC469822
0.6549 Remote Similarity NPC475900
0.6545 Remote Similarity NPC283409
0.6541 Remote Similarity NPC224623
0.6538 Remote Similarity NPC470516
0.6535 Remote Similarity NPC476204
0.6535 Remote Similarity NPC470478
0.6535 Remote Similarity NPC170084
0.6535 Remote Similarity NPC475182
0.6532 Remote Similarity NPC75287
0.6532 Remote Similarity NPC476992
0.6532 Remote Similarity NPC189126
0.6532 Remote Similarity NPC137414
0.6532 Remote Similarity NPC277583
0.6532 Remote Similarity NPC161674
0.6532 Remote Similarity NPC471384
0.6532 Remote Similarity NPC305267
0.6532 Remote Similarity NPC291903
0.6532 Remote Similarity NPC37134
0.6532 Remote Similarity NPC26626
0.6532 Remote Similarity NPC288205
0.6532 Remote Similarity NPC51465
0.6529 Remote Similarity NPC106760
0.6525 Remote Similarity NPC307846
0.6525 Remote Similarity NPC305157
0.6519 Remote Similarity NPC477236
0.6518 Remote Similarity NPC320089
0.6518 Remote Similarity NPC471483
0.6518 Remote Similarity NPC472874
0.6514 Remote Similarity NPC186148
0.6512 Remote Similarity NPC248202
0.6512 Remote Similarity NPC470477
0.6509 Remote Similarity NPC246076
0.6508 Remote Similarity NPC477464

  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 NPC475275 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
0.75 Intermediate Similarity NPD8268 Approved
0.75 Intermediate Similarity NPD8266 Approved
0.75 Intermediate Similarity NPD8267 Approved
0.75 Intermediate Similarity NPD8269 Approved
0.7478 Intermediate Similarity NPD8413 Clinical (unspecified phase)
0.6935 Remote Similarity NPD8517 Approved
0.6935 Remote Similarity NPD8516 Approved
0.6935 Remote Similarity NPD8515 Approved
0.68 Remote Similarity NPD8513 Phase 3
0.6777 Remote Similarity NPD8133 Approved
0.6417 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6239 Remote Similarity NPD8029 Clinical (unspecified phase)
0.623 Remote Similarity NPD6686 Approved
0.6195 Remote Similarity NPD6698 Approved
0.6195 Remote Similarity NPD46 Approved
0.6165 Remote Similarity NPD8074 Phase 3
0.6094 Remote Similarity NPD8295 Clinical (unspecified phase)
0.6061 Remote Similarity NPD8328 Phase 3
0.6 Remote Similarity NPD7983 Approved
0.5965 Remote Similarity NPD1695 Approved
0.5926 Remote Similarity NPD8448 Approved
0.592 Remote Similarity NPD8132 Clinical (unspecified phase)
0.5912 Remote Similarity NPD8391 Approved
0.5912 Remote Similarity NPD8392 Approved
0.5912 Remote Similarity NPD8390 Approved
0.5893 Remote Similarity NPD1733 Clinical (unspecified phase)
0.5852 Remote Similarity NPD8451 Approved
0.5839 Remote Similarity NPD7319 Approved
0.5833 Remote Similarity NPD8377 Approved
0.5833 Remote Similarity NPD8294 Approved
0.5798 Remote Similarity NPD7839 Suspended
0.5789 Remote Similarity NPD8379 Approved
0.5789 Remote Similarity NPD8335 Approved
0.5789 Remote Similarity NPD8033 Approved
0.5789 Remote Similarity NPD8380 Approved
0.5789 Remote Similarity NPD8296 Approved
0.5789 Remote Similarity NPD8378 Approved
0.5748 Remote Similarity NPD6371 Approved
0.5735 Remote Similarity NPD7507 Approved
0.5726 Remote Similarity NPD4056 Clinical (unspecified phase)
0.5726 Remote Similarity NPD4057 Clinical (unspecified phase)
0.5725 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5714 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5714 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5704 Remote Similarity NPD7830 Approved
0.5704 Remote Similarity NPD7829 Approved
0.5676 Remote Similarity NPD1779 Approved
0.5676 Remote Similarity NPD1780 Approved
0.5672 Remote Similarity NPD8444 Approved
0.5662 Remote Similarity NPD8340 Approved
0.5662 Remote Similarity NPD8342 Approved
0.5662 Remote Similarity NPD8299 Approved
0.5662 Remote Similarity NPD8341 Approved
0.5659 Remote Similarity NPD6053 Discontinued
0.5652 Remote Similarity NPD8337 Approved
0.5652 Remote Similarity NPD8336 Approved
0.5641 Remote Similarity NPD7838 Discovery
0.5635 Remote Similarity NPD6412 Phase 2
0.563 Remote Similarity NPD5282 Discontinued
0.56 Remote Similarity NPD8170 Clinical (unspecified phase)

  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