Structure

Physi-Chem Properties

Molecular Weight:  1092.57
Volume:  1065.647
LogP:  6.382
LogD:  4.34
LogS:  -6.307
# Rotatable Bonds:  2
TPSA:  192.82
# H-Bond Aceptor:  18
# H-Bond Donor:  1
# Rings:  16
# Heavy Atoms:  18

MedChem Properties

QED Drug-Likeness Score:  0.244
Synthetic Accessibility Score:  8.881
Fsp3:  0.9
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:  -5.108
MDCK Permeability:  0.00020986104209441692
Pgp-inhibitor:  0.003
Pgp-substrate:  1.0
Human Intestinal Absorption (HIA):  0.01
20% Bioavailability (F20%):  0.0
30% Bioavailability (F30%):  0.044

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.0
Plasma Protein Binding (PPB):  76.44650268554688%
Volume Distribution (VD):  -0.065
Pgp-substrate:  12.760726928710938%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.773
CYP2C19-inhibitor:  0.025
CYP2C19-substrate:  0.903
CYP2C9-inhibitor:  0.057
CYP2C9-substrate:  0.0
CYP2D6-inhibitor:  0.004
CYP2D6-substrate:  0.057
CYP3A4-inhibitor:  0.94
CYP3A4-substrate:  0.91

ADMET: Excretion

Clearance (CL):  14.495
Half-life (T1/2):  0.009

ADMET: Toxicity

hERG Blockers:  0.903
Human Hepatotoxicity (H-HT):  0.939
Drug-inuced Liver Injury (DILI):  0.983
AMES Toxicity:  0.359
Rat Oral Acute Toxicity:  0.996
Maximum Recommended Daily Dose:  0.998
Skin Sensitization:  0.967
Carcinogencity:  0.094
Eye Corrosion:  0.003
Eye Irritation:  0.011
Respiratory Toxicity:  0.983

Download Data

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

  Natural Product: NPC475537

Natural Product ID:  NPC475537
Common Name*:   REYYJCNLOIQWDF-AQIHPJOPSA-N
IUPAC Name:   n.a.
Synonyms:   Halichondrin B-1092
Standard InCHIKey:  REYYJCNLOIQWDF-AQIHPJOPSA-N
Standard InCHI:  InChI=1S/C60H84O18/c1-26-14-33-8-10-37-27(2)15-35(64-37)12-13-58-24-46-54(77-58)55-56(71-46)57(78-58)53-38(68-55)11-9-34(66-53)17-48(63)72-52-32(7)51-43(67-42(52)19-39(65-33)31(26)6)20-41-45(70-51)23-60(73-41)25-47-50(76-60)29(4)22-59(75-47)21-28(3)49-44(74-59)18-36(62)40(69-49)16-30(5)61/h26,28-29,32-47,49-57,62H,2,6,8-25H2,1,3-5,7H3/t26-,28+,29+,32+,33+,34-,35+,36-,37+,38+,39-,40-,41-,42+,43+,44+,45-,46-,47+,49+,50+,51+,52-,53+,54+,55+,56-,57+,58+,59-,60+/m1/s1
SMILES:  CC1CC2CCC3C(=C)CC(O3)CCC45CC6C(O4)C7C(O6)C(O5)C8C(O7)CCC(O8)CC(=O)OC9C(C3C(CC4C(O3)CC3(O4)CC4C(O3)C(CC3(O4)CC(C4C(O3)CC(C(O4)CC(=O)C)O)C)C)OC9CC(C1=C)O2)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL507657
PubChem CID:   44581725
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002204] C-glycosyl compounds

*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 = 0.00076 ug.mL-1 PMID[524784]

☑ 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 NPC475537 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 NPC308858
0.981 High Similarity NPC473849
0.981 High Similarity NPC312498
0.9429 High Similarity NPC475275
0.9429 High Similarity NPC473771
0.9115 High Similarity NPC475298
0.7946 Intermediate Similarity NPC470519
0.7946 Intermediate Similarity NPC231271
0.7845 Intermediate Similarity NPC126897
0.7845 Intermediate Similarity NPC297945
0.7672 Intermediate Similarity NPC313668
0.7672 Intermediate Similarity NPC315836
0.7547 Intermediate Similarity NPC51662
0.7459 Intermediate Similarity NPC109603
0.7459 Intermediate Similarity NPC93688
0.7411 Intermediate Similarity NPC304445
0.7411 Intermediate Similarity NPC236580
0.728 Intermediate Similarity NPC469812
0.728 Intermediate Similarity NPC183353
0.7265 Intermediate Similarity NPC476738
0.7265 Intermediate Similarity NPC478038
0.7265 Intermediate Similarity NPC476740
0.7241 Intermediate Similarity NPC473148
0.7222 Intermediate Similarity NPC314364
0.7217 Intermediate Similarity NPC67296
0.7213 Intermediate Similarity NPC54395
0.72 Intermediate Similarity NPC329008
0.72 Intermediate Similarity NPC108072
0.72 Intermediate Similarity NPC317635
0.7193 Intermediate Similarity NPC49833
0.7193 Intermediate Similarity NPC249171
0.7182 Intermediate Similarity NPC206614
0.7182 Intermediate Similarity NPC474323
0.7168 Intermediate Similarity NPC475375
0.7168 Intermediate Similarity NPC475525
0.7168 Intermediate Similarity NPC475164
0.7168 Intermediate Similarity NPC475241
0.7168 Intermediate Similarity NPC473605
0.7168 Intermediate Similarity NPC475540
0.7168 Intermediate Similarity NPC476066
0.7168 Intermediate Similarity NPC474297
0.7168 Intermediate Similarity NPC475593
0.7168 Intermediate Similarity NPC473765
0.7165 Intermediate Similarity NPC186339
0.7155 Intermediate Similarity NPC313569
0.7143 Intermediate Similarity NPC170880
0.7132 Intermediate Similarity NPC11732
0.712 Intermediate Similarity NPC207738
0.7109 Intermediate Similarity NPC473474
0.7105 Intermediate Similarity NPC261372
0.7105 Intermediate Similarity NPC263674
0.7105 Intermediate Similarity NPC58267
0.7099 Intermediate Similarity NPC311178
0.7099 Intermediate Similarity NPC43589
0.7099 Intermediate Similarity NPC222951
0.7099 Intermediate Similarity NPC300655
0.7097 Intermediate Similarity NPC156651
0.7097 Intermediate Similarity NPC471580
0.7094 Intermediate Similarity NPC473816
0.7094 Intermediate Similarity NPC474581
0.7094 Intermediate Similarity NPC309398
0.7094 Intermediate Similarity NPC475367
0.7091 Intermediate Similarity NPC92974
0.7059 Intermediate Similarity NPC287269
0.7049 Intermediate Similarity NPC470543
0.7045 Intermediate Similarity NPC322904
0.7045 Intermediate Similarity NPC233223
0.7045 Intermediate Similarity NPC196874
0.7045 Intermediate Similarity NPC475177
0.7045 Intermediate Similarity NPC324933
0.7045 Intermediate Similarity NPC183816
0.7045 Intermediate Similarity NPC319719
0.7045 Intermediate Similarity NPC473679
0.7045 Intermediate Similarity NPC475444
0.704 Intermediate Similarity NPC232237
0.704 Intermediate Similarity NPC105800
0.7031 Intermediate Similarity NPC256983
0.7031 Intermediate Similarity NPC160084
0.7018 Intermediate Similarity NPC476009
0.7018 Intermediate Similarity NPC158416
0.7018 Intermediate Similarity NPC76862
0.7018 Intermediate Similarity NPC39859
0.7018 Intermediate Similarity NPC470883
0.7016 Intermediate Similarity NPC469823
0.7016 Intermediate Similarity NPC469820
0.7009 Intermediate Similarity NPC80144
0.7009 Intermediate Similarity NPC60849
0.7009 Intermediate Similarity NPC472352
0.7009 Intermediate Similarity NPC477332
0.7008 Intermediate Similarity NPC477463
0.7008 Intermediate Similarity NPC51099
0.7008 Intermediate Similarity NPC293031
0.7008 Intermediate Similarity NPC275225
0.7008 Intermediate Similarity NPC475182
0.7008 Intermediate Similarity NPC68767
0.7 Intermediate Similarity NPC58219
0.7 Intermediate Similarity NPC177629
0.7 Intermediate Similarity NPC470516
0.7 Intermediate Similarity NPC193765
0.7 Intermediate Similarity NPC224414
0.6992 Remote Similarity NPC224623
0.6992 Remote Similarity NPC146563
0.6991 Remote Similarity NPC472198
0.6991 Remote Similarity NPC477345
0.6991 Remote Similarity NPC477348
0.6991 Remote Similarity NPC163409
0.6991 Remote Similarity NPC238264
0.6991 Remote Similarity NPC44682
0.6977 Remote Similarity NPC248202
0.6975 Remote Similarity NPC315070
0.697 Remote Similarity NPC469351
0.696 Remote Similarity NPC475514
0.696 Remote Similarity NPC110633
0.696 Remote Similarity NPC473452
0.696 Remote Similarity NPC33012
0.696 Remote Similarity NPC148417
0.696 Remote Similarity NPC136768
0.696 Remote Similarity NPC191827
0.696 Remote Similarity NPC69811
0.696 Remote Similarity NPC470876
0.696 Remote Similarity NPC102505
0.696 Remote Similarity NPC220160
0.696 Remote Similarity NPC85154
0.696 Remote Similarity NPC104137
0.696 Remote Similarity NPC473824
0.696 Remote Similarity NPC475119
0.696 Remote Similarity NPC309223
0.696 Remote Similarity NPC475209
0.696 Remote Similarity NPC123522
0.696 Remote Similarity NPC286457
0.696 Remote Similarity NPC8524
0.696 Remote Similarity NPC185466
0.6953 Remote Similarity NPC15918
0.6953 Remote Similarity NPC156789
0.6953 Remote Similarity NPC94072
0.6953 Remote Similarity NPC169816
0.6953 Remote Similarity NPC305771
0.6947 Remote Similarity NPC220838
0.6947 Remote Similarity NPC45606
0.6947 Remote Similarity NPC470476
0.694 Remote Similarity NPC477234
0.6935 Remote Similarity NPC469821
0.693 Remote Similarity NPC167893
0.693 Remote Similarity NPC475900
0.6929 Remote Similarity NPC473645
0.6929 Remote Similarity NPC110385
0.6929 Remote Similarity NPC37860
0.6929 Remote Similarity NPC476127
0.6929 Remote Similarity NPC144644
0.6929 Remote Similarity NPC153673
0.6929 Remote Similarity NPC142151
0.6929 Remote Similarity NPC268184
0.6929 Remote Similarity NPC267694
0.6929 Remote Similarity NPC476150
0.6923 Remote Similarity NPC470218
0.6923 Remote Similarity NPC273962
0.6909 Remote Similarity NPC186148
0.6905 Remote Similarity NPC470514
0.6905 Remote Similarity NPC469822
0.6905 Remote Similarity NPC237191
0.6905 Remote Similarity NPC36831
0.6905 Remote Similarity NPC475309
0.6905 Remote Similarity NPC470513
0.6903 Remote Similarity NPC471483
0.6903 Remote Similarity NPC320089
0.6899 Remote Similarity NPC202261
0.6899 Remote Similarity NPC106589
0.6894 Remote Similarity NPC477235
0.6891 Remote Similarity NPC474917
0.6885 Remote Similarity NPC106760
0.688 Remote Similarity NPC291903
0.688 Remote Similarity NPC305267
0.688 Remote Similarity NPC75287
0.688 Remote Similarity NPC51465
0.688 Remote Similarity NPC471384
0.688 Remote Similarity NPC189126
0.688 Remote Similarity NPC277583
0.688 Remote Similarity NPC288205
0.688 Remote Similarity NPC137414
0.688 Remote Similarity NPC161674
0.688 Remote Similarity NPC26626
0.688 Remote Similarity NPC37134
0.688 Remote Similarity NPC476992
0.6875 Remote Similarity NPC476204
0.6875 Remote Similarity NPC470478
0.6875 Remote Similarity NPC182900
0.6875 Remote Similarity NPC170084
0.6875 Remote Similarity NPC249553
0.687 Remote Similarity NPC54731
0.6866 Remote Similarity NPC475487
0.6864 Remote Similarity NPC106668
0.686 Remote Similarity NPC475960
0.6855 Remote Similarity NPC474410
0.6855 Remote Similarity NPC293658
0.685 Remote Similarity NPC471577
0.685 Remote Similarity NPC473386
0.685 Remote Similarity NPC477464
0.6846 Remote Similarity NPC476674
0.6846 Remote Similarity NPC470477
0.6846 Remote Similarity NPC144625

  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 NPC475537 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
0.7851 Intermediate Similarity NPD8269 Approved
0.7851 Intermediate Similarity NPD8268 Approved
0.7851 Intermediate Similarity NPD8267 Approved
0.7851 Intermediate Similarity NPD8266 Approved
0.7845 Intermediate Similarity NPD8413 Clinical (unspecified phase)
0.728 Intermediate Similarity NPD8515 Approved
0.728 Intermediate Similarity NPD8516 Approved
0.728 Intermediate Similarity NPD8517 Approved
0.7143 Intermediate Similarity NPD8513 Phase 3
0.7131 Intermediate Similarity NPD8133 Approved
0.6639 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6585 Remote Similarity NPD6686 Approved
0.6579 Remote Similarity NPD46 Approved
0.6579 Remote Similarity NPD6698 Approved
0.6515 Remote Similarity NPD8328 Phase 3
0.6493 Remote Similarity NPD8074 Phase 3
0.6471 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6434 Remote Similarity NPD8295 Clinical (unspecified phase)
0.64 Remote Similarity NPD8132 Clinical (unspecified phase)
0.6379 Remote Similarity NPD7983 Approved
0.625 Remote Similarity NPD8448 Approved
0.6232 Remote Similarity NPD8391 Approved
0.6232 Remote Similarity NPD8390 Approved
0.6232 Remote Similarity NPD8392 Approved
0.622 Remote Similarity NPD6371 Approved
0.619 Remote Similarity NPD5345 Clinical (unspecified phase)
0.6176 Remote Similarity NPD8451 Approved
0.6165 Remote Similarity NPD8294 Approved
0.6165 Remote Similarity NPD8377 Approved
0.6159 Remote Similarity NPD7319 Approved
0.6119 Remote Similarity NPD8378 Approved
0.6119 Remote Similarity NPD8033 Approved
0.6119 Remote Similarity NPD8444 Approved
0.6119 Remote Similarity NPD8296 Approved
0.6119 Remote Similarity NPD8335 Approved
0.6119 Remote Similarity NPD8380 Approved
0.6119 Remote Similarity NPD8379 Approved
0.6111 Remote Similarity NPD6412 Phase 2
0.6083 Remote Similarity NPD1698 Clinical (unspecified phase)
0.608 Remote Similarity NPD4056 Clinical (unspecified phase)
0.608 Remote Similarity NPD8170 Clinical (unspecified phase)
0.608 Remote Similarity NPD4057 Clinical (unspecified phase)
0.6061 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6058 Remote Similarity NPD7507 Approved
0.6033 Remote Similarity NPD7839 Suspended
0.6029 Remote Similarity NPD7830 Approved
0.6029 Remote Similarity NPD7829 Approved
0.6017 Remote Similarity NPD7838 Discovery
0.6 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5985 Remote Similarity NPD8341 Approved
0.5985 Remote Similarity NPD8340 Approved
0.5985 Remote Similarity NPD8299 Approved
0.5985 Remote Similarity NPD8342 Approved
0.5956 Remote Similarity NPD8080 Discontinued
0.592 Remote Similarity NPD8138 Approved
0.592 Remote Similarity NPD8139 Approved
0.592 Remote Similarity NPD8083 Approved
0.592 Remote Similarity NPD8082 Approved
0.592 Remote Similarity NPD8086 Approved
0.592 Remote Similarity NPD8085 Approved
0.592 Remote Similarity NPD8084 Approved
0.5906 Remote Similarity NPD8393 Approved
0.5893 Remote Similarity NPD7329 Approved
0.5878 Remote Similarity NPD6053 Discontinued
0.5873 Remote Similarity NPD8275 Approved
0.5873 Remote Similarity NPD8276 Approved
0.5868 Remote Similarity NPD5282 Discontinued
0.5862 Remote Similarity NPD7966 Clinical (unspecified phase)
0.5857 Remote Similarity NPD7736 Approved
0.5827 Remote Similarity NPD8081 Approved
0.5821 Remote Similarity NPD7115 Discovery
0.5806 Remote Similarity NPD4225 Approved
0.5798 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5798 Remote Similarity NPD6101 Approved
0.5797 Remote Similarity NPD7642 Approved
0.5793 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5786 Remote Similarity NPD7078 Approved
0.5786 Remote Similarity NPD8293 Discontinued
0.5785 Remote Similarity NPD5779 Approved
0.5785 Remote Similarity NPD5778 Approved
0.5778 Remote Similarity NPD7328 Approved
0.5778 Remote Similarity NPD7327 Approved
0.5766 Remote Similarity NPD6921 Approved
0.5755 Remote Similarity NPD7492 Approved
0.5735 Remote Similarity NPD7516 Approved
0.5724 Remote Similarity NPD8415 Approved
0.5714 Remote Similarity NPD8273 Phase 1
0.5714 Remote Similarity NPD6616 Approved
0.5702 Remote Similarity NPD6411 Approved
0.5693 Remote Similarity NPD6054 Approved
0.5693 Remote Similarity NPD6059 Approved
0.5667 Remote Similarity NPD1695 Approved
0.5662 Remote Similarity NPD7641 Discontinued
0.5652 Remote Similarity NPD7503 Approved
0.5612 Remote Similarity NPD6370 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