Structure

Physi-Chem Properties

Molecular Weight:  1140.54
Volume:  1092.234
LogP:  7.243
LogD:  4.734
LogS:  -6.606
# Rotatable Bonds:  2
TPSA:  184.98
# H-Bond Aceptor:  18
# H-Bond Donor:  1
# Rings:  17
# Heavy Atoms:  19

MedChem Properties

QED Drug-Likeness Score:  0.178
Synthetic Accessibility Score:  8.952
Fsp3:  0.918
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:  -5.208
MDCK Permeability:  0.00028395606204867363
Pgp-inhibitor:  0.0
Pgp-substrate:  1.0
Human Intestinal Absorption (HIA):  0.008
20% Bioavailability (F20%):  0.0
30% Bioavailability (F30%):  0.012

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.0
Plasma Protein Binding (PPB):  89.51605987548828%
Volume Distribution (VD):  -0.228
Pgp-substrate:  8.433062553405762%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.799
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.897
CYP2C9-inhibitor:  0.041
CYP2C9-substrate:  0.0
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.056
CYP3A4-inhibitor:  0.931
CYP3A4-substrate:  0.914

ADMET: Excretion

Clearance (CL):  13.562
Half-life (T1/2):  0.005

ADMET: Toxicity

hERG Blockers:  0.945
Human Hepatotoxicity (H-HT):  0.903
Drug-inuced Liver Injury (DILI):  0.986
AMES Toxicity:  0.292
Rat Oral Acute Toxicity:  0.994
Maximum Recommended Daily Dose:  0.997
Skin Sensitization:  0.972
Carcinogencity:  0.082
Eye Corrosion:  0.003
Eye Irritation:  0.007
Respiratory Toxicity:  0.971

Download Data

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

  Natural Product: NPC475298

Natural Product ID:  NPC475298
Common Name*:   ZUHKWHQWUPFTAS-XWAHEJASSA-N
IUPAC Name:   n.a.
Synonyms:   Halichondrin B-1140
Standard InCHIKey:  ZUHKWHQWUPFTAS-XWAHEJASSA-N
Standard InCHI:  InChI=1S/C61H85ClO18/c1-26-13-32-7-9-36-27(2)14-34(65-36)11-12-59-23-47-55(79-59)56-57(73-47)58(80-59)54-37(70-56)10-8-33(67-54)15-49(64)74-53-31(6)52-44(69-43(53)16-38(66-32)30(26)5)19-42-46(72-52)22-61(75-42)24-48-51(78-61)29(4)21-60(77-48)20-28(3)50-45(76-60)18-40-41(71-50)17-39(68-40)35(63)25-62/h26,28-29,31-48,50-58,63H,2,5,7-25H2,1,3-4,6H3/t26-,28+,29+,31+,32+,33-,34+,35?,36+,37+,38-,39?,40-,41-,42-,43+,44+,45+,46-,47-,48+,50+,51+,52+,53-,54+,55+,56+,57-,58+,59+,60-,61+/m1/s1
SMILES:  ClCC(C1O[C@H]2[C@@H](C1)O[C@@H]1[C@H](C2)O[C@]2(C[C@@H]1C)O[C@H]1C[C@@]3(O[C@H]1[C@H](C2)C)C[C@@H]1[C@H](O3)C[C@H]2[C@@H](O1)[C@H](C)[C@@H]1[C@@H](O2)C[C@H]2O[C@@H](CC[C@@H]3O[C@H](CC3=C)CC[C@@]34O[C@H]5[C@H]6O[C@@H](CC(=O)O1)CC[C@@H]6O[C@@H]1[C@H]5O[C@@H]([C@@H]1O3)C4)C[C@H](C2=C)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL503145
PubChem CID:   44581724
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 = 0.002 ug.mL-1 PMID[570791]

☑ 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 NPC475298 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
0.9279 High Similarity NPC473849
0.9279 High Similarity NPC312498
0.9115 High Similarity NPC475537
0.9115 High Similarity NPC308858
0.875 High Similarity NPC475275
0.875 High Similarity NPC473771
0.825 Intermediate Similarity NPC109603
0.825 Intermediate Similarity NPC93688
0.7542 Intermediate Similarity NPC231271
0.7542 Intermediate Similarity NPC470519
0.7317 Intermediate Similarity NPC126897
0.7317 Intermediate Similarity NPC297945
0.7154 Intermediate Similarity NPC313668
0.7154 Intermediate Similarity NPC315836
0.7143 Intermediate Similarity NPC51662
0.6953 Remote Similarity NPC329869
0.6911 Remote Similarity NPC476738
0.6911 Remote Similarity NPC476740
0.6891 Remote Similarity NPC304445
0.6891 Remote Similarity NPC236580
0.6875 Remote Similarity NPC54395
0.6842 Remote Similarity NPC314364
0.6822 Remote Similarity NPC470466
0.6818 Remote Similarity NPC469812
0.6818 Remote Similarity NPC183353
0.6807 Remote Similarity NPC476066
0.6807 Remote Similarity NPC473765
0.6807 Remote Similarity NPC475241
0.6807 Remote Similarity NPC475593
0.6807 Remote Similarity NPC475540
0.6807 Remote Similarity NPC475164
0.6807 Remote Similarity NPC475375
0.6807 Remote Similarity NPC473605
0.6807 Remote Similarity NPC475525
0.6769 Remote Similarity NPC156651
0.6748 Remote Similarity NPC309398
0.6748 Remote Similarity NPC474581
0.6748 Remote Similarity NPC473816
0.6748 Remote Similarity NPC473148
0.6748 Remote Similarity NPC475367
0.6744 Remote Similarity NPC226608
0.6744 Remote Similarity NPC88867
0.6742 Remote Similarity NPC317635
0.6742 Remote Similarity NPC329008
0.6721 Remote Similarity NPC67296
0.672 Remote Similarity NPC287269
0.6719 Remote Similarity NPC470543
0.6694 Remote Similarity NPC249171
0.6694 Remote Similarity NPC49833
0.6692 Remote Similarity NPC477463
0.6692 Remote Similarity NPC275225
0.6692 Remote Similarity NPC68767
0.6692 Remote Similarity NPC293031
0.6692 Remote Similarity NPC469820
0.6692 Remote Similarity NPC469823
0.6692 Remote Similarity NPC170880
0.6692 Remote Similarity NPC51099
0.6667 Remote Similarity NPC311178
0.6667 Remote Similarity NPC474297
0.6667 Remote Similarity NPC300655
0.6667 Remote Similarity NPC207738
0.6667 Remote Similarity NPC43589
0.6667 Remote Similarity NPC474323
0.6667 Remote Similarity NPC193765
0.6667 Remote Similarity NPC224414
0.6667 Remote Similarity NPC146563
0.6667 Remote Similarity NPC222951
0.6667 Remote Similarity NPC89018
0.6667 Remote Similarity NPC68248
0.6667 Remote Similarity NPC206614
0.6641 Remote Similarity NPC220160
0.6641 Remote Similarity NPC123522
0.6641 Remote Similarity NPC475514
0.6641 Remote Similarity NPC102505
0.6641 Remote Similarity NPC69811
0.6641 Remote Similarity NPC471580
0.6641 Remote Similarity NPC470876
0.6641 Remote Similarity NPC33012
0.6641 Remote Similarity NPC475209
0.6641 Remote Similarity NPC309223
0.6641 Remote Similarity NPC185466
0.6641 Remote Similarity NPC286457
0.6641 Remote Similarity NPC473452
0.6641 Remote Similarity NPC8524
0.6641 Remote Similarity NPC191827
0.6641 Remote Similarity NPC104137
0.6641 Remote Similarity NPC85154
0.664 Remote Similarity NPC315070
0.664 Remote Similarity NPC478038
0.6639 Remote Similarity NPC477345
0.6639 Remote Similarity NPC477348
0.6639 Remote Similarity NPC44682
0.6639 Remote Similarity NPC163409
0.6639 Remote Similarity NPC238264
0.6639 Remote Similarity NPC472198
0.6637 Remote Similarity NPC60849
0.6637 Remote Similarity NPC472352
0.6637 Remote Similarity NPC477332
0.6619 Remote Similarity NPC475444
0.6619 Remote Similarity NPC183816
0.6619 Remote Similarity NPC324933
0.6619 Remote Similarity NPC319719
0.6619 Remote Similarity NPC322904
0.6619 Remote Similarity NPC475177
0.6619 Remote Similarity NPC473679
0.6619 Remote Similarity NPC196874
0.6619 Remote Similarity NPC233223
0.6617 Remote Similarity NPC108072
0.6617 Remote Similarity NPC267694
0.6617 Remote Similarity NPC144644
0.6617 Remote Similarity NPC110385
0.6617 Remote Similarity NPC142151
0.6617 Remote Similarity NPC153673
0.6617 Remote Similarity NPC476150
0.6617 Remote Similarity NPC476127
0.6617 Remote Similarity NPC37860
0.6615 Remote Similarity NPC469821
0.6614 Remote Similarity NPC475191
0.6612 Remote Similarity NPC263674
0.6612 Remote Similarity NPC58267
0.6612 Remote Similarity NPC261372
0.6593 Remote Similarity NPC106589
0.6593 Remote Similarity NPC186339
0.6593 Remote Similarity NPC202261
0.6593 Remote Similarity NPC256983
0.6591 Remote Similarity NPC469822
0.6591 Remote Similarity NPC237191
0.6591 Remote Similarity NPC105800
0.6591 Remote Similarity NPC232237
0.6589 Remote Similarity NPC470468
0.6581 Remote Similarity NPC92974
0.6569 Remote Similarity NPC11732
0.6567 Remote Similarity NPC475182
0.6567 Remote Similarity NPC476204
0.6567 Remote Similarity NPC170084
0.6565 Remote Similarity NPC26626
0.6565 Remote Similarity NPC305267
0.6565 Remote Similarity NPC75287
0.6565 Remote Similarity NPC189126
0.6565 Remote Similarity NPC476992
0.6565 Remote Similarity NPC51465
0.6565 Remote Similarity NPC137414
0.6565 Remote Similarity NPC288205
0.6562 Remote Similarity NPC106760
0.6555 Remote Similarity NPC320089
0.6555 Remote Similarity NPC471483
0.6544 Remote Similarity NPC248202
0.6544 Remote Similarity NPC473474
0.6541 Remote Similarity NPC477464
0.6541 Remote Similarity NPC473386
0.6541 Remote Similarity NPC471577
0.6538 Remote Similarity NPC474410
0.6538 Remote Similarity NPC293658
0.6535 Remote Similarity NPC128210
0.6532 Remote Similarity NPC80144
0.6532 Remote Similarity NPC313569
0.6525 Remote Similarity NPC477234
0.6522 Remote Similarity NPC472268
0.6522 Remote Similarity NPC472270
0.6522 Remote Similarity NPC472269
0.6522 Remote Similarity NPC112492
0.6522 Remote Similarity NPC23020
0.6522 Remote Similarity NPC220838
0.6522 Remote Similarity NPC470476
0.6522 Remote Similarity NPC45606
0.6519 Remote Similarity NPC43842
0.6515 Remote Similarity NPC110633
0.6515 Remote Similarity NPC475119
0.6515 Remote Similarity NPC473824
0.6515 Remote Similarity NPC136768
0.6515 Remote Similarity NPC148417
0.6512 Remote Similarity NPC204392
0.6512 Remote Similarity NPC240734
0.6512 Remote Similarity NPC272242
0.6512 Remote Similarity NPC11035
0.6512 Remote Similarity NPC1876
0.6512 Remote Similarity NPC470467
0.6512 Remote Similarity NPC91838
0.6512 Remote Similarity NPC275668
0.6512 Remote Similarity NPC170294
0.6496 Remote Similarity NPC58219
0.6496 Remote Similarity NPC177629
0.6496 Remote Similarity NPC273962
0.6496 Remote Similarity NPC470218
0.6493 Remote Similarity NPC268184
0.6493 Remote Similarity NPC207243
0.6493 Remote Similarity NPC476991
0.6493 Remote Similarity NPC473645
0.6493 Remote Similarity NPC233391
0.6493 Remote Similarity NPC198325
0.6489 Remote Similarity NPC476068
0.6489 Remote Similarity NPC121816
0.6489 Remote Similarity NPC471550
0.6489 Remote Similarity NPC57484
0.6489 Remote Similarity NPC224381
0.6489 Remote Similarity NPC473714
0.6489 Remote Similarity NPC71065
0.6489 Remote Similarity NPC4328
0.6489 Remote Similarity NPC227551
0.6489 Remote Similarity NPC164389

  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 NPC475298 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
0.7317 Intermediate Similarity NPD8413 Clinical (unspecified phase)
0.7209 Intermediate Similarity NPD8267 Approved
0.7209 Intermediate Similarity NPD8268 Approved
0.7209 Intermediate Similarity NPD8266 Approved
0.7209 Intermediate Similarity NPD8269 Approved
0.6818 Remote Similarity NPD8515 Approved
0.6818 Remote Similarity NPD8517 Approved
0.6818 Remote Similarity NPD8516 Approved
0.6797 Remote Similarity NPD8133 Approved
0.6692 Remote Similarity NPD8513 Phase 3
0.6279 Remote Similarity NPD6686 Approved
0.625 Remote Similarity NPD6698 Approved
0.625 Remote Similarity NPD46 Approved
0.6202 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6099 Remote Similarity NPD8074 Phase 3
0.6066 Remote Similarity NPD7983 Approved
0.6032 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6029 Remote Similarity NPD8295 Clinical (unspecified phase)
0.6 Remote Similarity NPD8328 Phase 3
0.5903 Remote Similarity NPD7319 Approved
0.5899 Remote Similarity NPD8294 Approved
0.5899 Remote Similarity NPD8377 Approved
0.5894 Remote Similarity NPD8384 Approved
0.5874 Remote Similarity NPD8448 Approved
0.5865 Remote Similarity NPD8132 Clinical (unspecified phase)
0.5862 Remote Similarity NPD8390 Approved
0.5862 Remote Similarity NPD8392 Approved
0.5862 Remote Similarity NPD8391 Approved
0.5857 Remote Similarity NPD8296 Approved
0.5857 Remote Similarity NPD8033 Approved
0.5857 Remote Similarity NPD8380 Approved
0.5857 Remote Similarity NPD8378 Approved
0.5857 Remote Similarity NPD8335 Approved
0.5857 Remote Similarity NPD8379 Approved
0.5804 Remote Similarity NPD7507 Approved
0.5804 Remote Similarity NPD8451 Approved
0.5797 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5775 Remote Similarity NPD7830 Approved
0.5775 Remote Similarity NPD7829 Approved
0.5748 Remote Similarity NPD7839 Suspended
0.5745 Remote Similarity NPD8444 Approved
0.5726 Remote Similarity NPD7838 Discovery
0.5724 Remote Similarity NPD6033 Approved
0.5714 Remote Similarity NPD6412 Phase 2
0.5704 Remote Similarity NPD6371 Approved
0.5682 Remote Similarity NPD8170 Clinical (unspecified phase)
0.5682 Remote Similarity NPD4057 Clinical (unspecified phase)
0.5682 Remote Similarity NPD4056 Clinical (unspecified phase)
0.5672 Remote Similarity NPD5345 Clinical (unspecified phase)
0.5646 Remote Similarity NPD5956 Approved
0.5634 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5625 Remote Similarity NPD8340 Approved
0.5625 Remote Similarity NPD8299 Approved
0.5625 Remote Similarity NPD8341 Approved
0.5625 Remote Similarity NPD8342 Approved
0.562 Remote Similarity NPD6053 Discontinued

  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