Structure

Physi-Chem Properties

Molecular Weight:  517.29
Volume:  508.913
LogP:  2.226
LogD:  2.669
LogS:  -1.898
# Rotatable Bonds:  10
TPSA:  134.17
# H-Bond Aceptor:  11
# H-Bond Donor:  3
# Rings:  3
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.279
Synthetic Accessibility Score:  5.71
Fsp3:  0.88
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:  -5.071
MDCK Permeability:  3.5197717807022855e-05
Pgp-inhibitor:  0.724
Pgp-substrate:  0.958
Human Intestinal Absorption (HIA):  0.069
20% Bioavailability (F20%):  0.025
30% Bioavailability (F30%):  0.192

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.062
Plasma Protein Binding (PPB):  50.079864501953125%
Volume Distribution (VD):  0.821
Pgp-substrate:  47.51463317871094%

ADMET: Metabolism

CYP1A2-inhibitor:  0.003
CYP1A2-substrate:  0.127
CYP2C19-inhibitor:  0.007
CYP2C19-substrate:  0.604
CYP2C9-inhibitor:  0.003
CYP2C9-substrate:  0.004
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.116
CYP3A4-inhibitor:  0.014
CYP3A4-substrate:  0.725

ADMET: Excretion

Clearance (CL):  6.041
Half-life (T1/2):  0.794

ADMET: Toxicity

hERG Blockers:  0.041
Human Hepatotoxicity (H-HT):  0.321
Drug-inuced Liver Injury (DILI):  0.92
AMES Toxicity:  0.719
Rat Oral Acute Toxicity:  0.093
Maximum Recommended Daily Dose:  0.661
Skin Sensitization:  0.249
Carcinogencity:  0.094
Eye Corrosion:  0.003
Eye Irritation:  0.008
Respiratory Toxicity:  0.032

Download Data

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

  Natural Product: NPC225978

Natural Product ID:  NPC225978
Common Name*:   Mycalamide B
IUPAC Name:   (2S)-N-[(4S,4aS,6R,8S,8aR)-6-[(2S)-3-hydroxy-2-methoxypropyl]-8-methoxy-7,7-dimethyl-4a,6,8,8a-tetrahydro-4H-pyrano[3,2-d][1,3]dioxin-4-yl]-2-hydroxy-2-[(2R,5R,6R)-2-methoxy-5,6-dimethyl-4-methylideneoxan-2-yl]acetamide
Synonyms:  
Standard InCHIKey:  AAABMNXUOFPYQK-GRMLSQNXSA-N
Standard InCHI:  InChI=1S/C25H43NO10/c1-13-10-25(32-8,36-15(3)14(13)2)20(28)22(29)26-23-19-18(33-12-34-23)21(31-7)24(4,5)17(35-19)9-16(11-27)30-6/h14-21,23,27-28H,1,9-12H2,2-8H3,(H,26,29)/t14-,15-,16+,17-,18+,19+,20-,21-,23+,25-/m1/s1
SMILES:  C=C1C[C@@]([C@@H](C(=N[C@@H]2[C@@H]3[C@@H]([C@H](C(C)(C)[C@@H](C[C@@H](CO)OC)O3)OC)OCO2)O)O)(OC)O[C@H](C)[C@@H]1C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL499036
PubChem CID:   11060358
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000002] Organoheterocyclic compounds
      • [CHEMONTID:0002011] Pyranodioxins

*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
NPO32868 Mycale sp. Species Mycalidae Eukaryota n.a. New Zealand n.a. PMID[10843597]
NPO32868 Mycale sp. Species Mycalidae Eukaryota n.a. Thai n.a. PMID[12608869]
NPO32868 Mycale sp. Species Mycalidae Eukaryota n.a. n.a. n.a. PMID[19845338]
NPO32868 Mycale sp. Species Mycalidae Eukaryota n.a. n.a. n.a. PMID[31833368]
NPO32868 Mycale sp. Species Mycalidae Eukaryota n.a. n.a. n.a. PMID[9599273]

☑ 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 = 1.3 nM PMID[516136]
NPT857 Cell Line LLC-PK1 Sus scrofa IC50 = 19.43 nM PMID[516136]
NPT519 Cell Line SH-SY5Y Homo sapiens IC50 = 6.42 nM PMID[516136]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 9.3 nM PMID[516136]

☑ 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 NPC225978 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 NPC255175
1.0 High Similarity NPC271207
1.0 High Similarity NPC206711
0.9674 High Similarity NPC189629
0.8058 Intermediate Similarity NPC477198
0.7843 Intermediate Similarity NPC475646
0.7755 Intermediate Similarity NPC470284
0.7745 Intermediate Similarity NPC475503
0.7708 Intermediate Similarity NPC476523
0.7525 Intermediate Similarity NPC475603
0.7525 Intermediate Similarity NPC61894
0.7436 Intermediate Similarity NPC469943
0.7379 Intermediate Similarity NPC470283
0.7212 Intermediate Similarity NPC70323
0.7212 Intermediate Similarity NPC256570
0.7212 Intermediate Similarity NPC17290
0.7212 Intermediate Similarity NPC192066
0.7212 Intermediate Similarity NPC262312
0.7212 Intermediate Similarity NPC35269
0.7212 Intermediate Similarity NPC3568
0.7212 Intermediate Similarity NPC23454
0.7207 Intermediate Similarity NPC475150
0.7182 Intermediate Similarity NPC475918
0.7143 Intermediate Similarity NPC473578
0.7075 Intermediate Similarity NPC197294
0.7075 Intermediate Similarity NPC183449
0.7075 Intermediate Similarity NPC8098
0.7075 Intermediate Similarity NPC45313
0.7063 Intermediate Similarity NPC280941
0.7063 Intermediate Similarity NPC235772
0.704 Intermediate Similarity NPC119794
0.704 Intermediate Similarity NPC73829
0.7019 Intermediate Similarity NPC473581
0.7019 Intermediate Similarity NPC15851
0.7019 Intermediate Similarity NPC111567
0.7019 Intermediate Similarity NPC473950
0.7019 Intermediate Similarity NPC475125
0.7019 Intermediate Similarity NPC282705
0.7019 Intermediate Similarity NPC186840
0.7019 Intermediate Similarity NPC309898
0.7019 Intermediate Similarity NPC263545
0.7019 Intermediate Similarity NPC473604
0.7019 Intermediate Similarity NPC182632
0.7018 Intermediate Similarity NPC29501
0.6961 Remote Similarity NPC470282
0.696 Remote Similarity NPC475472
0.696 Remote Similarity NPC139585
0.6957 Remote Similarity NPC469865
0.6929 Remote Similarity NPC75318
0.6923 Remote Similarity NPC209047
0.6923 Remote Similarity NPC43074
0.6923 Remote Similarity NPC74672
0.6923 Remote Similarity NPC242503
0.6923 Remote Similarity NPC139782
0.6899 Remote Similarity NPC243680
0.6899 Remote Similarity NPC200788
0.6887 Remote Similarity NPC54961
0.6887 Remote Similarity NPC158445
0.6887 Remote Similarity NPC156782
0.6887 Remote Similarity NPC157353
0.6887 Remote Similarity NPC282088
0.6875 Remote Similarity NPC145899
0.6857 Remote Similarity NPC270005
0.6857 Remote Similarity NPC208537
0.685 Remote Similarity NPC76999
0.685 Remote Similarity NPC477072
0.6846 Remote Similarity NPC180770
0.6846 Remote Similarity NPC302276
0.6794 Remote Similarity NPC210729
0.6794 Remote Similarity NPC172365
0.6794 Remote Similarity NPC82931
0.6767 Remote Similarity NPC141669
0.6742 Remote Similarity NPC162910
0.6735 Remote Similarity NPC316807
0.6729 Remote Similarity NPC72817
0.6729 Remote Similarity NPC477927
0.67 Remote Similarity NPC16090
0.6697 Remote Similarity NPC76486
0.6692 Remote Similarity NPC475394
0.6692 Remote Similarity NPC475152
0.6692 Remote Similarity NPC475584
0.6667 Remote Similarity NPC166279
0.6667 Remote Similarity NPC477199
0.6642 Remote Similarity NPC284625
0.6642 Remote Similarity NPC193579
0.6642 Remote Similarity NPC298469
0.6642 Remote Similarity NPC475892
0.6642 Remote Similarity NPC69176
0.6634 Remote Similarity NPC20072
0.6593 Remote Similarity NPC298067
0.6593 Remote Similarity NPC214821
0.6591 Remote Similarity NPC265908
0.6587 Remote Similarity NPC329919
0.6587 Remote Similarity NPC477793
0.6579 Remote Similarity NPC201128
0.6577 Remote Similarity NPC64348
0.6577 Remote Similarity NPC91497
0.6571 Remote Similarity NPC248312
0.656 Remote Similarity NPC94881
0.656 Remote Similarity NPC48886
0.656 Remote Similarity NPC265275
0.6542 Remote Similarity NPC302584
0.6525 Remote Similarity NPC314306
0.6522 Remote Similarity NPC36463
0.6522 Remote Similarity NPC298005
0.6518 Remote Similarity NPC263756
0.6518 Remote Similarity NPC117714
0.6496 Remote Similarity NPC61717
0.6496 Remote Similarity NPC244380
0.6486 Remote Similarity NPC56071
0.6486 Remote Similarity NPC477928
0.6486 Remote Similarity NPC70733
0.6481 Remote Similarity NPC67398
0.6481 Remote Similarity NPC91654
0.6481 Remote Similarity NPC474835
0.6481 Remote Similarity NPC474792
0.648 Remote Similarity NPC296686
0.646 Remote Similarity NPC76497
0.646 Remote Similarity NPC272015
0.646 Remote Similarity NPC30289
0.646 Remote Similarity NPC213674
0.646 Remote Similarity NPC256133
0.6455 Remote Similarity NPC90583
0.6455 Remote Similarity NPC472989
0.6449 Remote Similarity NPC477865
0.6449 Remote Similarity NPC477866
0.6449 Remote Similarity NPC159876
0.6436 Remote Similarity NPC471420
0.6436 Remote Similarity NPC100697
0.6435 Remote Similarity NPC309448
0.6434 Remote Similarity NPC15249
0.6434 Remote Similarity NPC25455
0.6422 Remote Similarity NPC305160
0.6404 Remote Similarity NPC123796
0.6396 Remote Similarity NPC278506
0.6396 Remote Similarity NPC473890
0.6396 Remote Similarity NPC240372
0.6396 Remote Similarity NPC243728
0.6396 Remote Similarity NPC470684
0.6396 Remote Similarity NPC470683
0.6385 Remote Similarity NPC122819
0.6383 Remote Similarity NPC477760
0.6383 Remote Similarity NPC477758
0.6383 Remote Similarity NPC477754
0.6383 Remote Similarity NPC477761
0.6383 Remote Similarity NPC477759
0.6381 Remote Similarity NPC470836
0.6379 Remote Similarity NPC317534
0.6379 Remote Similarity NPC230507
0.6379 Remote Similarity NPC78034
0.6379 Remote Similarity NPC190395
0.6379 Remote Similarity NPC283829
0.6379 Remote Similarity NPC94272
0.6379 Remote Similarity NPC257964
0.6379 Remote Similarity NPC113044
0.6379 Remote Similarity NPC470432
0.6379 Remote Similarity NPC14704
0.6379 Remote Similarity NPC305423
0.6379 Remote Similarity NPC161676
0.6372 Remote Similarity NPC188453
0.6372 Remote Similarity NPC470168
0.6372 Remote Similarity NPC42320
0.6364 Remote Similarity NPC297058
0.6364 Remote Similarity NPC172197
0.6364 Remote Similarity NPC274293
0.6355 Remote Similarity NPC473058
0.6349 Remote Similarity NPC469494
0.6348 Remote Similarity NPC470768
0.6348 Remote Similarity NPC471435
0.6348 Remote Similarity NPC230948
0.6348 Remote Similarity NPC74035
0.6348 Remote Similarity NPC109792
0.6348 Remote Similarity NPC57065
0.6348 Remote Similarity NPC475521
0.6348 Remote Similarity NPC476361
0.6348 Remote Similarity NPC148603
0.6348 Remote Similarity NPC221562
0.6348 Remote Similarity NPC54521
0.6348 Remote Similarity NPC473734
0.6348 Remote Similarity NPC470885
0.6348 Remote Similarity NPC476360
0.6348 Remote Similarity NPC187400
0.6348 Remote Similarity NPC471434
0.6344 Remote Similarity NPC147292
0.6339 Remote Similarity NPC158088
0.6336 Remote Similarity NPC150057
0.6336 Remote Similarity NPC147753
0.6325 Remote Similarity NPC98696
0.6325 Remote Similarity NPC126147
0.6316 Remote Similarity NPC312553
0.6316 Remote Similarity NPC288694
0.6316 Remote Similarity NPC136816
0.6316 Remote Similarity NPC159036
0.6306 Remote Similarity NPC207617
0.6296 Remote Similarity NPC261990
0.6296 Remote Similarity NPC474249
0.6293 Remote Similarity NPC470763
0.6293 Remote Similarity NPC474569
0.6293 Remote Similarity NPC269627
0.6293 Remote Similarity NPC173859

  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 NPC225978 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
0.7054 Intermediate Similarity NPD8174 Phase 2
0.6923 Remote Similarity NPD8522 Clinical (unspecified phase)
0.6638 Remote Similarity NPD6421 Discontinued
0.6525 Remote Similarity NPD6430 Approved
0.6525 Remote Similarity NPD6429 Approved
0.6435 Remote Similarity NPD5357 Phase 1
0.6385 Remote Similarity NPD8449 Approved
0.6371 Remote Similarity NPD8267 Approved
0.6371 Remote Similarity NPD8266 Approved
0.6371 Remote Similarity NPD8269 Approved
0.6371 Remote Similarity NPD8268 Approved
0.6357 Remote Similarity NPD8390 Approved
0.6357 Remote Similarity NPD8391 Approved
0.6357 Remote Similarity NPD8392 Approved
0.6336 Remote Similarity NPD8450 Suspended
0.632 Remote Similarity NPD6436 Phase 3
0.6311 Remote Similarity NPD8137 Clinical (unspecified phase)
0.6293 Remote Similarity NPD5376 Approved
0.6271 Remote Similarity NPD8305 Approved
0.6271 Remote Similarity NPD8306 Approved
0.622 Remote Similarity NPD8299 Approved
0.622 Remote Similarity NPD8342 Approved
0.622 Remote Similarity NPD8341 Approved
0.622 Remote Similarity NPD8340 Approved
0.6216 Remote Similarity NPD5378 Approved
0.6216 Remote Similarity NPD5377 Approved
0.6216 Remote Similarity NPD5381 Approved
0.6172 Remote Similarity NPD8451 Approved
0.6161 Remote Similarity NPD6428 Approved
0.6154 Remote Similarity NPD6640 Phase 3
0.6129 Remote Similarity NPD7641 Discontinued
0.6124 Remote Similarity NPD8448 Approved
0.6122 Remote Similarity NPD3187 Discontinued
0.6121 Remote Similarity NPD8276 Approved
0.6121 Remote Similarity NPD8275 Approved
0.6111 Remote Similarity NPD8274 Clinical (unspecified phase)
0.6102 Remote Similarity NPD8307 Discontinued
0.6102 Remote Similarity NPD8140 Approved
0.6082 Remote Similarity NPD9445 Approved
0.6063 Remote Similarity NPD8080 Discontinued
0.6034 Remote Similarity NPD8083 Approved
0.6034 Remote Similarity NPD8138 Approved
0.6034 Remote Similarity NPD8139 Approved
0.6034 Remote Similarity NPD8085 Approved
0.6034 Remote Similarity NPD8084 Approved
0.6034 Remote Similarity NPD8086 Approved
0.6034 Remote Similarity NPD8082 Approved
0.6019 Remote Similarity NPD4759 Clinical (unspecified phase)
0.6017 Remote Similarity NPD8393 Approved
0.6 Remote Similarity NPD3168 Discontinued
0.5983 Remote Similarity NPD1407 Approved
0.595 Remote Similarity NPD8087 Discontinued
0.5935 Remote Similarity NPD8133 Approved
0.5932 Remote Similarity NPD8081 Approved
0.5929 Remote Similarity NPD7844 Discontinued
0.5917 Remote Similarity NPD6686 Approved
0.5909 Remote Similarity NPD3716 Discontinued
0.5906 Remote Similarity NPD8345 Approved
0.5906 Remote Similarity NPD8346 Approved
0.5906 Remote Similarity NPD8347 Approved
0.5897 Remote Similarity NPD7140 Approved
0.5897 Remote Similarity NPD7139 Approved
0.5897 Remote Similarity NPD7141 Clinical (unspecified phase)
0.5891 Remote Similarity NPD7829 Approved
0.5891 Remote Similarity NPD7830 Approved
0.5877 Remote Similarity NPD3189 Approved
0.5877 Remote Similarity NPD3190 Approved
0.5877 Remote Similarity NPD3191 Approved
0.5865 Remote Similarity NPD6914 Discontinued
0.5862 Remote Similarity NPD4836 Approved
0.5862 Remote Similarity NPD4835 Approved
0.5862 Remote Similarity NPD4838 Approved
0.5862 Remote Similarity NPD4837 Approved
0.5847 Remote Similarity NPD8045 Clinical (unspecified phase)
0.5833 Remote Similarity NPD6412 Phase 2
0.5806 Remote Similarity NPD3731 Phase 3
0.5804 Remote Similarity NPD7625 Phase 1
0.5772 Remote Similarity NPD8413 Clinical (unspecified phase)
0.5766 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5758 Remote Similarity NPD8074 Phase 3
0.5752 Remote Similarity NPD8171 Discontinued
0.5752 Remote Similarity NPD1447 Phase 3
0.5752 Remote Similarity NPD5781 Clinical (unspecified phase)
0.5752 Remote Similarity NPD1446 Phase 3
0.5738 Remote Similarity NPD6941 Approved
0.5736 Remote Similarity NPD8444 Approved
0.5714 Remote Similarity NPD4832 Approved
0.5714 Remote Similarity NPD4831 Approved
0.5714 Remote Similarity NPD4830 Approved
0.5693 Remote Similarity NPD8415 Approved
0.569 Remote Similarity NPD4282 Approved
0.5676 Remote Similarity NPD618 Clinical (unspecified phase)
0.5659 Remote Similarity NPD8377 Approved
0.5659 Remote Similarity NPD8294 Approved
0.5649 Remote Similarity NPD7642 Approved
0.5641 Remote Similarity NPD2255 Approved
0.5641 Remote Similarity NPD8029 Clinical (unspecified phase)
0.5636 Remote Similarity NPD3200 Clinical (unspecified phase)
0.562 Remote Similarity NPD4211 Phase 1
0.5615 Remote Similarity NPD8378 Approved
0.5615 Remote Similarity NPD8380 Approved
0.5615 Remote Similarity NPD8296 Approved
0.5615 Remote Similarity NPD8379 Approved
0.5615 Remote Similarity NPD8033 Approved
0.5615 Remote Similarity NPD8335 Approved
0.561 Remote Similarity NPD8132 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