Structure

Physi-Chem Properties

Molecular Weight:  1122.58
Volume:  1085.813
LogP:  6.487
LogD:  4.384
LogS:  -6.195
# Rotatable Bonds:  2
TPSA:  205.21
# H-Bond Aceptor:  19
# H-Bond Donor:  2
# Rings:  17
# Heavy Atoms:  19

MedChem Properties

QED Drug-Likeness Score:  0.265
Synthetic Accessibility Score:  8.939
Fsp3:  0.918
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:  -5.226
MDCK Permeability:  0.0002830788434948772
Pgp-inhibitor:  0.0
Pgp-substrate:  1.0
Human Intestinal Absorption (HIA):  0.012
20% Bioavailability (F20%):  0.0
30% Bioavailability (F30%):  0.008

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.001
Plasma Protein Binding (PPB):  71.90506744384766%
Volume Distribution (VD):  -0.258
Pgp-substrate:  13.588504791259766%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.641
CYP2C19-inhibitor:  0.016
CYP2C19-substrate:  0.845
CYP2C9-inhibitor:  0.033
CYP2C9-substrate:  0.0
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.053
CYP3A4-inhibitor:  0.913
CYP3A4-substrate:  0.908

ADMET: Excretion

Clearance (CL):  12.379
Half-life (T1/2):  0.01

ADMET: Toxicity

hERG Blockers:  0.927
Human Hepatotoxicity (H-HT):  0.885
Drug-inuced Liver Injury (DILI):  0.984
AMES Toxicity:  0.331
Rat Oral Acute Toxicity:  0.997
Maximum Recommended Daily Dose:  0.997
Skin Sensitization:  0.972
Carcinogencity:  0.081
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: NPC473849

Natural Product ID:  NPC473849
Common Name*:   Homohalichondrin B
IUPAC Name:   n.a.
Synonyms:  
Standard InCHIKey:  LMZKVILFCFSDGK-XWAHEJASSA-N
Standard InCHI:  InChI=1S/C61H86O19/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/h26,28-29,31-48,50-58,62-63H,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:  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)CC3C(O4)CC(O3)C(CO)O)C)C)OC9CC(C1=C)O2)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL453453
PubChem CID:   44581723
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 T/C = 285.0 n.a. PMID[525672]
NPT168 Cell Line P388 Mus musculus IC50 = 0.00022 ug.mL-1 PMID[525673]

☑ 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 NPC473849 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 NPC312498
0.981 High Similarity NPC475537
0.981 High Similarity NPC308858
0.9423 High Similarity NPC473771
0.9423 High Similarity NPC475275
0.9279 High Similarity NPC475298
0.8091 Intermediate Similarity NPC470519
0.8091 Intermediate Similarity NPC231271
0.7826 Intermediate Similarity NPC126897
0.7826 Intermediate Similarity NPC297945
0.7692 Intermediate Similarity NPC51662
0.7652 Intermediate Similarity NPC313668
0.7652 Intermediate Similarity NPC315836
0.7583 Intermediate Similarity NPC109603
0.7583 Intermediate Similarity NPC93688
0.7391 Intermediate Similarity NPC476740
0.7391 Intermediate Similarity NPC476738
0.7387 Intermediate Similarity NPC236580
0.7387 Intermediate Similarity NPC304445
0.7358 Intermediate Similarity NPC314364
0.7333 Intermediate Similarity NPC54395
0.7297 Intermediate Similarity NPC475164
0.7297 Intermediate Similarity NPC475375
0.7297 Intermediate Similarity NPC475525
0.7297 Intermediate Similarity NPC475593
0.7297 Intermediate Similarity NPC475540
0.7297 Intermediate Similarity NPC475241
0.7297 Intermediate Similarity NPC473765
0.7297 Intermediate Similarity NPC473605
0.7297 Intermediate Similarity NPC476066
0.7258 Intermediate Similarity NPC183353
0.7258 Intermediate Similarity NPC469812
0.7217 Intermediate Similarity NPC473148
0.7217 Intermediate Similarity NPC474581
0.7217 Intermediate Similarity NPC473816
0.7217 Intermediate Similarity NPC309398
0.7217 Intermediate Similarity NPC475367
0.7213 Intermediate Similarity NPC156651
0.7193 Intermediate Similarity NPC67296
0.7179 Intermediate Similarity NPC287269
0.7177 Intermediate Similarity NPC317635
0.7177 Intermediate Similarity NPC329008
0.7168 Intermediate Similarity NPC49833
0.7168 Intermediate Similarity NPC249171
0.7167 Intermediate Similarity NPC470543
0.7156 Intermediate Similarity NPC474323
0.7156 Intermediate Similarity NPC206614
0.7143 Intermediate Similarity NPC60849
0.7143 Intermediate Similarity NPC477332
0.7143 Intermediate Similarity NPC472352
0.7143 Intermediate Similarity NPC474297
0.7131 Intermediate Similarity NPC469820
0.7131 Intermediate Similarity NPC469823
0.712 Intermediate Similarity NPC275225
0.712 Intermediate Similarity NPC68767
0.712 Intermediate Similarity NPC51099
0.712 Intermediate Similarity NPC170880
0.712 Intermediate Similarity NPC293031
0.712 Intermediate Similarity NPC477463
0.7119 Intermediate Similarity NPC193765
0.7119 Intermediate Similarity NPC224414
0.7117 Intermediate Similarity NPC472198
0.7117 Intermediate Similarity NPC477345
0.7117 Intermediate Similarity NPC477348
0.7117 Intermediate Similarity NPC163409
0.7117 Intermediate Similarity NPC238264
0.7117 Intermediate Similarity NPC44682
0.7107 Intermediate Similarity NPC146563
0.7097 Intermediate Similarity NPC207738
0.7094 Intermediate Similarity NPC478038
0.7094 Intermediate Similarity NPC315070
0.708 Intermediate Similarity NPC261372
0.708 Intermediate Similarity NPC263674
0.708 Intermediate Similarity NPC58267
0.7077 Intermediate Similarity NPC311178
0.7077 Intermediate Similarity NPC300655
0.7077 Intermediate Similarity NPC43589
0.7077 Intermediate Similarity NPC222951
0.7073 Intermediate Similarity NPC473452
0.7073 Intermediate Similarity NPC475514
0.7073 Intermediate Similarity NPC185466
0.7073 Intermediate Similarity NPC85154
0.7073 Intermediate Similarity NPC286457
0.7073 Intermediate Similarity NPC8524
0.7073 Intermediate Similarity NPC470876
0.7073 Intermediate Similarity NPC123522
0.7073 Intermediate Similarity NPC191827
0.7073 Intermediate Similarity NPC102505
0.7073 Intermediate Similarity NPC104137
0.7073 Intermediate Similarity NPC220160
0.7073 Intermediate Similarity NPC475209
0.7073 Intermediate Similarity NPC69811
0.7073 Intermediate Similarity NPC33012
0.7073 Intermediate Similarity NPC309223
0.7073 Intermediate Similarity NPC471580
0.7064 Intermediate Similarity NPC92974
0.7049 Intermediate Similarity NPC469821
0.704 Intermediate Similarity NPC108072
0.704 Intermediate Similarity NPC144644
0.704 Intermediate Similarity NPC37860
0.704 Intermediate Similarity NPC110385
0.704 Intermediate Similarity NPC153673
0.704 Intermediate Similarity NPC142151
0.704 Intermediate Similarity NPC476150
0.704 Intermediate Similarity NPC267694
0.704 Intermediate Similarity NPC476127
0.7027 Intermediate Similarity NPC471483
0.7027 Intermediate Similarity NPC320089
0.7023 Intermediate Similarity NPC196874
0.7023 Intermediate Similarity NPC473679
0.7023 Intermediate Similarity NPC233223
0.7023 Intermediate Similarity NPC475444
0.7023 Intermediate Similarity NPC324933
0.7023 Intermediate Similarity NPC183816
0.7023 Intermediate Similarity NPC475177
0.7023 Intermediate Similarity NPC322904
0.7023 Intermediate Similarity NPC319719
0.7016 Intermediate Similarity NPC105800
0.7016 Intermediate Similarity NPC232237
0.7016 Intermediate Similarity NPC469822
0.7016 Intermediate Similarity NPC237191
0.7008 Intermediate Similarity NPC202261
0.7008 Intermediate Similarity NPC106589
0.7008 Intermediate Similarity NPC256983
0.7008 Intermediate Similarity NPC186339
0.7 Intermediate Similarity NPC106760
0.6992 Remote Similarity NPC305267
0.6992 Remote Similarity NPC189126
0.6992 Remote Similarity NPC75287
0.6992 Remote Similarity NPC476992
0.6992 Remote Similarity NPC26626
0.6992 Remote Similarity NPC137414
0.6992 Remote Similarity NPC288205
0.6992 Remote Similarity NPC51465
0.6984 Remote Similarity NPC476204
0.6984 Remote Similarity NPC170084
0.6984 Remote Similarity NPC475182
0.6983 Remote Similarity NPC313569
0.6983 Remote Similarity NPC80144
0.6977 Remote Similarity NPC11732
0.6972 Remote Similarity NPC177629
0.6972 Remote Similarity NPC58219
0.6967 Remote Similarity NPC293658
0.6967 Remote Similarity NPC474410
0.696 Remote Similarity NPC471577
0.696 Remote Similarity NPC477464
0.696 Remote Similarity NPC473386
0.6953 Remote Similarity NPC248202
0.6953 Remote Similarity NPC473474
0.6952 Remote Similarity NPC477331
0.6952 Remote Similarity NPC119583
0.6952 Remote Similarity NPC307400
0.6952 Remote Similarity NPC297768
0.6952 Remote Similarity NPC472202
0.6952 Remote Similarity NPC123204
0.6952 Remote Similarity NPC290012
0.6952 Remote Similarity NPC259294
0.6952 Remote Similarity NPC472201
0.6952 Remote Similarity NPC44782
0.6952 Remote Similarity NPC89843
0.6952 Remote Similarity NPC475270
0.6952 Remote Similarity NPC472205
0.6952 Remote Similarity NPC477317
0.6952 Remote Similarity NPC475327
0.6952 Remote Similarity NPC169345
0.6952 Remote Similarity NPC477319
0.6952 Remote Similarity NPC173328
0.6952 Remote Similarity NPC186992
0.6952 Remote Similarity NPC184915
0.6952 Remote Similarity NPC475667
0.6952 Remote Similarity NPC27289
0.6952 Remote Similarity NPC477347
0.6952 Remote Similarity NPC224953
0.6952 Remote Similarity NPC472200
0.6952 Remote Similarity NPC183888
0.6952 Remote Similarity NPC143421
0.6952 Remote Similarity NPC115013
0.6952 Remote Similarity NPC269318
0.6952 Remote Similarity NPC472204
0.6952 Remote Similarity NPC238056
0.6952 Remote Similarity NPC476087
0.6952 Remote Similarity NPC477318
0.6952 Remote Similarity NPC472203
0.6952 Remote Similarity NPC126685
0.6944 Remote Similarity NPC474949
0.6944 Remote Similarity NPC474762
0.6944 Remote Similarity NPC475019
0.6944 Remote Similarity NPC476015
0.6942 Remote Similarity NPC204392
0.6942 Remote Similarity NPC91838
0.6942 Remote Similarity NPC11035
0.6942 Remote Similarity NPC272242
0.6942 Remote Similarity NPC1876
0.6942 Remote Similarity NPC240734
0.6942 Remote Similarity NPC275668
0.6937 Remote Similarity NPC472199
0.6937 Remote Similarity NPC477349
0.6935 Remote Similarity NPC148417
0.6935 Remote Similarity NPC473824
0.6935 Remote Similarity NPC136768

  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 NPC473849 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
0.7826 Intermediate Similarity NPD8413 Clinical (unspecified phase)
0.7686 Intermediate Similarity NPD8268 Approved
0.7686 Intermediate Similarity NPD8266 Approved
0.7686 Intermediate Similarity NPD8267 Approved
0.7686 Intermediate Similarity NPD8269 Approved
0.7258 Intermediate Similarity NPD8517 Approved
0.7258 Intermediate Similarity NPD8515 Approved
0.7258 Intermediate Similarity NPD8516 Approved
0.725 Intermediate Similarity NPD8133 Approved
0.712 Intermediate Similarity NPD8513 Phase 3
0.6696 Remote Similarity NPD6698 Approved
0.6696 Remote Similarity NPD46 Approved
0.6694 Remote Similarity NPD6686 Approved
0.6612 Remote Similarity NPD7899 Clinical (unspecified phase)
0.6491 Remote Similarity NPD7983 Approved
0.6466 Remote Similarity NPD8074 Phase 3
0.6441 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6406 Remote Similarity NPD8295 Clinical (unspecified phase)
0.6364 Remote Similarity NPD8328 Phase 3
0.626 Remote Similarity NPD8294 Approved
0.626 Remote Similarity NPD8377 Approved
0.625 Remote Similarity NPD7319 Approved
0.624 Remote Similarity NPD8132 Clinical (unspecified phase)
0.6222 Remote Similarity NPD8448 Approved
0.6212 Remote Similarity NPD8033 Approved
0.6212 Remote Similarity NPD8379 Approved
0.6212 Remote Similarity NPD8296 Approved
0.6212 Remote Similarity NPD8380 Approved
0.6212 Remote Similarity NPD8335 Approved
0.6212 Remote Similarity NPD8378 Approved
0.6204 Remote Similarity NPD8391 Approved
0.6204 Remote Similarity NPD8392 Approved
0.6204 Remote Similarity NPD8390 Approved
0.6154 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6148 Remote Similarity NPD8451 Approved
0.6148 Remote Similarity NPD7507 Approved
0.6134 Remote Similarity NPD7839 Suspended
0.6121 Remote Similarity NPD7838 Discovery
0.6119 Remote Similarity NPD7830 Approved
0.6119 Remote Similarity NPD7829 Approved
0.609 Remote Similarity NPD8444 Approved
0.608 Remote Similarity NPD6412 Phase 2
0.6063 Remote Similarity NPD6371 Approved
0.6048 Remote Similarity NPD4056 Clinical (unspecified phase)
0.6048 Remote Similarity NPD8170 Clinical (unspecified phase)
0.6048 Remote Similarity NPD4057 Clinical (unspecified phase)
0.6032 Remote Similarity NPD5345 Clinical (unspecified phase)
0.597 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5969 Remote Similarity NPD6053 Discontinued
0.5956 Remote Similarity NPD8299 Approved
0.5956 Remote Similarity NPD8340 Approved
0.5956 Remote Similarity NPD8341 Approved
0.5956 Remote Similarity NPD8342 Approved
0.5926 Remote Similarity NPD8080 Discontinued
0.5917 Remote Similarity NPD1698 Clinical (unspecified phase)
0.5897 Remote Similarity NPD6101 Approved
0.5897 Remote Similarity NPD5764 Clinical (unspecified phase)
0.5882 Remote Similarity NPD5779 Approved
0.5882 Remote Similarity NPD5778 Approved
0.5865 Remote Similarity NPD7327 Approved
0.5865 Remote Similarity NPD7328 Approved
0.5856 Remote Similarity NPD7329 Approved
0.5833 Remote Similarity NPD7966 Clinical (unspecified phase)
0.5827 Remote Similarity NPD7736 Approved
0.5821 Remote Similarity NPD7516 Approved
0.5798 Remote Similarity NPD6411 Approved
0.5797 Remote Similarity NPD8273 Phase 1
0.5772 Remote Similarity NPD4225 Approved
0.5764 Remote Similarity NPD8387 Clinical (unspecified phase)
0.576 Remote Similarity NPD8084 Approved
0.576 Remote Similarity NPD8139 Approved
0.576 Remote Similarity NPD8138 Approved
0.576 Remote Similarity NPD8086 Approved
0.576 Remote Similarity NPD8085 Approved
0.576 Remote Similarity NPD8082 Approved
0.576 Remote Similarity NPD8083 Approved
0.5755 Remote Similarity NPD7078 Approved
0.5755 Remote Similarity NPD8293 Discontinued
0.5748 Remote Similarity NPD8393 Approved
0.5735 Remote Similarity NPD7503 Approved
0.5725 Remote Similarity NPD7492 Approved
0.5714 Remote Similarity NPD8276 Approved
0.5714 Remote Similarity NPD8275 Approved
0.5702 Remote Similarity NPD5282 Discontinued
0.5694 Remote Similarity NPD8415 Approved
0.5683 Remote Similarity NPD6616 Approved
0.5672 Remote Similarity NPD7115 Discovery
0.5669 Remote Similarity NPD8081 Approved
0.5662 Remote Similarity NPD6059 Approved
0.5662 Remote Similarity NPD6054 Approved
0.5652 Remote Similarity NPD7642 Approved
0.563 Remote Similarity NPD1695 Approved
0.562 Remote Similarity NPD8171 Discontinued
0.562 Remote Similarity NPD6921 Approved
0.5615 Remote Similarity NPD4061 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