Structure

Physi-Chem Properties

Molecular Weight:  706.51
Volume:  756.496
LogP:  3.37
LogD:  3.61
LogS:  -4.714
# Rotatable Bonds:  20
TPSA:  146.58
# H-Bond Aceptor:  10
# H-Bond Donor:  5
# Rings:  3
# Heavy Atoms:  10

MedChem Properties

QED Drug-Likeness Score:  0.09
Synthetic Accessibility Score:  6.075
Fsp3:  0.85
Lipinski Rule-of-5:  Accepted
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:  -4.95
MDCK Permeability:  5.438102743937634e-05
Pgp-inhibitor:  0.967
Pgp-substrate:  0.995
Human Intestinal Absorption (HIA):  0.779
20% Bioavailability (F20%):  0.503
30% Bioavailability (F30%):  0.888

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.025
Plasma Protein Binding (PPB):  97.2999038696289%
Volume Distribution (VD):  0.919
Pgp-substrate:  2.3704404830932617%

ADMET: Metabolism

CYP1A2-inhibitor:  0.001
CYP1A2-substrate:  0.08
CYP2C19-inhibitor:  0.044
CYP2C19-substrate:  0.891
CYP2C9-inhibitor:  0.008
CYP2C9-substrate:  0.043
CYP2D6-inhibitor:  0.003
CYP2D6-substrate:  0.24
CYP3A4-inhibitor:  0.926
CYP3A4-substrate:  0.807

ADMET: Excretion

Clearance (CL):  9.372
Half-life (T1/2):  0.105

ADMET: Toxicity

hERG Blockers:  0.088
Human Hepatotoxicity (H-HT):  0.932
Drug-inuced Liver Injury (DILI):  0.037
AMES Toxicity:  0.017
Rat Oral Acute Toxicity:  0.975
Maximum Recommended Daily Dose:  0.936
Skin Sensitization:  0.756
Carcinogencity:  0.014
Eye Corrosion:  0.003
Eye Irritation:  0.005
Respiratory Toxicity:  0.029

Download Data

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

  Natural Product: NPC475646

Natural Product ID:  NPC475646
Common Name*:   Bistramide D
IUPAC Name:   3-hydroxy-N-[3-[8-[(E)-6-hydroxy-3,5-dimethylhept-4-enyl]-3-methyl-1,7-dioxaspiro[5.5]undecan-2-yl]propyl]-4-[[2-[6-[(E,2R)-2-hydroxypent-3-enyl]-3-methyloxan-2-yl]acetyl]amino]-2-methylbutanamide
Synonyms:   Bistramide D
Standard InCHIKey:  MPAHXQNOKKDZFI-PAZXGEJJSA-N
Standard InCHI:  InChI=1S/C40H70N2O8/c1-8-11-32(44)23-34-17-15-27(3)37(48-34)24-38(46)42-25-35(45)30(6)39(47)41-21-10-13-36-28(4)18-20-40(50-36)19-9-12-33(49-40)16-14-26(2)22-29(5)31(7)43/h8,11,22,26-28,30-37,43-45H,9-10,12-21,23-25H2,1-7H3,(H,41,47)(H,42,46)/b11-8+,29-22+/t26?,27?,28?,30?,31?,32-,33?,34?,35?,36?,37?,40?/m0/s1
SMILES:  CC=CC(CC1CCC(C(O1)CC(=O)NCC(C(C)C(=O)NCCCC2C(CCC3(O2)CCCC(O3)CCC(C)C=C(C)C(C)O)C)O)C)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL510222
PubChem CID:   44559679
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0000265] Carboxylic acids and derivatives
        • [CHEMONTID:0000013] Amino acids, peptides, and analogues
          • [CHEMONTID:0000347] Amino acids and derivatives
            • [CHEMONTID:0001880] Gamma amino acids and derivatives

*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
NPO22842 Lissoclinum bistratum Species Didemnidae Eukaryota n.a. n.a. n.a. PMID[12608858]
NPO22842 Lissoclinum bistratum Species Didemnidae Eukaryota n.a. n.a. n.a. PMID[7807120]
NPO22842 Lissoclinum bistratum Species Didemnidae Eukaryota n.a. n.a. n.a. Database[UNPD]

☑ 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
NPT91 Cell Line KB Homo sapiens IC50 = 10.0 ug.mL-1 PMID[507246]
NPT168 Cell Line P388 Mus musculus IC50 = 0.36 ug.mL-1 PMID[507246]
NPT168 Cell Line P388 Mus musculus IC50 = 5.82 ug.mL-1 PMID[507246]
NPT319 Cell Line B16 Mus musculus IC50 = 0.1 ug.mL-1 PMID[507246]
NPT139 Cell Line HT-29 Homo sapiens IC50 = 2.76 ug.mL-1 PMID[507246]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. IC50 = 3.43 ug.mL-1 PMID[507246]
NPT20529 NON-MOLECULAR NON-PROTEIN TARGET n.a. T/C = 53.0 % PMID[507246]

☑ 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 NPC475646 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
0.967 High Similarity NPC475503
0.89 High Similarity NPC475150
0.8738 High Similarity NPC469865
0.8447 Intermediate Similarity NPC473578
0.7843 Intermediate Similarity NPC225978
0.7843 Intermediate Similarity NPC271207
0.7843 Intermediate Similarity NPC255175
0.7843 Intermediate Similarity NPC206711
0.7723 Intermediate Similarity NPC189629
0.77 Intermediate Similarity NPC256570
0.77 Intermediate Similarity NPC17290
0.77 Intermediate Similarity NPC3568
0.77 Intermediate Similarity NPC192066
0.7692 Intermediate Similarity NPC477198
0.7576 Intermediate Similarity NPC209047
0.7576 Intermediate Similarity NPC139782
0.7576 Intermediate Similarity NPC242503
0.7576 Intermediate Similarity NPC43074
0.7576 Intermediate Similarity NPC74672
0.7549 Intermediate Similarity NPC197294
0.7549 Intermediate Similarity NPC8098
0.7549 Intermediate Similarity NPC183449
0.7525 Intermediate Similarity NPC262312
0.7525 Intermediate Similarity NPC35269
0.7525 Intermediate Similarity NPC23454
0.7525 Intermediate Similarity NPC70323
0.75 Intermediate Similarity NPC111567
0.75 Intermediate Similarity NPC186840
0.75 Intermediate Similarity NPC15851
0.75 Intermediate Similarity NPC473950
0.75 Intermediate Similarity NPC473604
0.75 Intermediate Similarity NPC263545
0.75 Intermediate Similarity NPC309898
0.75 Intermediate Similarity NPC473581
0.75 Intermediate Similarity NPC475125
0.7455 Intermediate Similarity NPC29501
0.74 Intermediate Similarity NPC477866
0.74 Intermediate Similarity NPC477865
0.7379 Intermediate Similarity NPC45313
0.7353 Intermediate Similarity NPC282088
0.7353 Intermediate Similarity NPC157353
0.7353 Intermediate Similarity NPC156782
0.7353 Intermediate Similarity NPC54961
0.7353 Intermediate Similarity NPC158445
0.7327 Intermediate Similarity NPC182632
0.7327 Intermediate Similarity NPC475603
0.7327 Intermediate Similarity NPC282705
0.7327 Intermediate Similarity NPC61894
0.729 Intermediate Similarity NPC55336
0.7248 Intermediate Similarity NPC315426
0.7156 Intermediate Similarity NPC475918
0.7119 Intermediate Similarity NPC469943
0.6863 Remote Similarity NPC470284
0.6847 Remote Similarity NPC201128
0.68 Remote Similarity NPC477199
0.6768 Remote Similarity NPC477385
0.6768 Remote Similarity NPC477390
0.6765 Remote Similarity NPC313658
0.6765 Remote Similarity NPC316138
0.6757 Remote Similarity NPC74035
0.6739 Remote Similarity NPC103712
0.6739 Remote Similarity NPC291196
0.6726 Remote Similarity NPC474969
0.6726 Remote Similarity NPC476034
0.6721 Remote Similarity NPC469494
0.6699 Remote Similarity NPC248312
0.6699 Remote Similarity NPC316186
0.6694 Remote Similarity NPC477793
0.6694 Remote Similarity NPC329919
0.6667 Remote Similarity NPC476084
0.6667 Remote Similarity NPC476075
0.6667 Remote Similarity NPC474891
0.6638 Remote Similarity NPC268327
0.6638 Remote Similarity NPC295444
0.6638 Remote Similarity NPC273215
0.6637 Remote Similarity NPC250187
0.6636 Remote Similarity NPC175531
0.6634 Remote Similarity NPC476523
0.6632 Remote Similarity NPC288086
0.6612 Remote Similarity NPC469515
0.6604 Remote Similarity NPC109406
0.66 Remote Similarity NPC20072
0.6574 Remote Similarity NPC165332
0.6574 Remote Similarity NPC195645
0.6574 Remote Similarity NPC180722
0.6567 Remote Similarity NPC214821
0.6567 Remote Similarity NPC298067
0.6549 Remote Similarity NPC135216
0.6549 Remote Similarity NPC101106
0.6545 Remote Similarity NPC64348
0.6542 Remote Similarity NPC470283
0.6535 Remote Similarity NPC228638
0.6514 Remote Similarity NPC240372
0.6512 Remote Similarity NPC280941
0.6512 Remote Similarity NPC235772
0.6509 Remote Similarity NPC302584
0.6509 Remote Similarity NPC471324
0.6509 Remote Similarity NPC206679
0.6509 Remote Similarity NPC472199
0.6509 Remote Similarity NPC114172
0.6509 Remote Similarity NPC472197
0.6505 Remote Similarity NPC477387
0.6505 Remote Similarity NPC477389
0.6496 Remote Similarity NPC279383
0.6496 Remote Similarity NPC314306
0.6486 Remote Similarity NPC154132
0.6486 Remote Similarity NPC475157
0.6486 Remote Similarity NPC57586
0.6486 Remote Similarity NPC2313
0.6486 Remote Similarity NPC475655
0.6486 Remote Similarity NPC471637
0.6484 Remote Similarity NPC119794
0.6484 Remote Similarity NPC314361
0.6484 Remote Similarity NPC73829
0.6475 Remote Similarity NPC242692
0.6471 Remote Similarity NPC274293
0.6471 Remote Similarity NPC172197
0.6471 Remote Similarity NPC244380
0.6471 Remote Similarity NPC477554
0.6471 Remote Similarity NPC61717
0.6449 Remote Similarity NPC472196
0.6449 Remote Similarity NPC472195
0.6449 Remote Similarity NPC159092
0.6449 Remote Similarity NPC238090
0.6442 Remote Similarity NPC199382
0.6442 Remote Similarity NPC125142
0.6442 Remote Similarity NPC477388
0.6442 Remote Similarity NPC477386
0.6441 Remote Similarity NPC475988
0.6439 Remote Similarity NPC180770
0.6435 Remote Similarity NPC471636
0.6435 Remote Similarity NPC287572
0.6423 Remote Similarity NPC472458
0.6422 Remote Similarity NPC90583
0.6417 Remote Similarity NPC477553
0.6408 Remote Similarity NPC471494
0.6406 Remote Similarity NPC475472
0.6404 Remote Similarity NPC315070
0.64 Remote Similarity NPC100697
0.6392 Remote Similarity NPC217095
0.6392 Remote Similarity NPC264417
0.6389 Remote Similarity NPC472198
0.6389 Remote Similarity NPC5418
0.6389 Remote Similarity NPC159698
0.6387 Remote Similarity NPC471645
0.6385 Remote Similarity NPC75318
0.6379 Remote Similarity NPC133625
0.6377 Remote Similarity NPC298005
0.6377 Remote Similarity NPC36463
0.6372 Remote Similarity NPC162354
0.6372 Remote Similarity NPC197736
0.6364 Remote Similarity NPC243680
0.6364 Remote Similarity NPC477555
0.6364 Remote Similarity NPC200788
0.6354 Remote Similarity NPC55652
0.6346 Remote Similarity NPC470836
0.6344 Remote Similarity NPC259299
0.6343 Remote Similarity NPC162910
0.6339 Remote Similarity NPC474873
0.6337 Remote Similarity NPC82799
0.6336 Remote Similarity NPC145899
0.6327 Remote Similarity NPC469880
0.6325 Remote Similarity NPC472359
0.6325 Remote Similarity NPC127578
0.6321 Remote Similarity NPC159369
0.6321 Remote Similarity NPC39290
0.632 Remote Similarity NPC314451
0.632 Remote Similarity NPC313342
0.632 Remote Similarity NPC314512
0.632 Remote Similarity NPC313333
0.6316 Remote Similarity NPC470768
0.6316 Remote Similarity NPC302276
0.6311 Remote Similarity NPC477515
0.6311 Remote Similarity NPC314268
0.6311 Remote Similarity NPC313802
0.6311 Remote Similarity NPC67917
0.6308 Remote Similarity NPC76999
0.6296 Remote Similarity NPC67398
0.6296 Remote Similarity NPC91654
0.6296 Remote Similarity NPC474792
0.6286 Remote Similarity NPC471056
0.6286 Remote Similarity NPC471055
0.6283 Remote Similarity NPC50815
0.6283 Remote Similarity NPC471083
0.6283 Remote Similarity NPC247060
0.6281 Remote Similarity NPC316325
0.6279 Remote Similarity NPC139585
0.6277 Remote Similarity NPC305698
0.6275 Remote Similarity NPC474312
0.6275 Remote Similarity NPC224072
0.6275 Remote Similarity NPC39966
0.6273 Remote Similarity NPC175614
0.6271 Remote Similarity NPC126897
0.6271 Remote Similarity NPC297945
0.6269 Remote Similarity NPC172365
0.6269 Remote Similarity NPC210729
0.6269 Remote Similarity NPC82931
0.6261 Remote Similarity NPC470767
0.6261 Remote Similarity NPC476738
0.6261 Remote Similarity NPC476740

  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 NPC475646 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
0.7576 Intermediate Similarity NPD8522 Clinical (unspecified phase)
0.6903 Remote Similarity NPD6421 Discontinued
0.6574 Remote Similarity NPD7839 Suspended
0.6549 Remote Similarity NPD4211 Phase 1
0.6549 Remote Similarity NPD5357 Phase 1
0.6496 Remote Similarity NPD6429 Approved
0.6496 Remote Similarity NPD6430 Approved
0.6457 Remote Similarity NPD8392 Approved
0.6457 Remote Similarity NPD8391 Approved
0.6457 Remote Similarity NPD8390 Approved
0.6455 Remote Similarity NPD8029 Clinical (unspecified phase)
0.6449 Remote Similarity NPD5781 Clinical (unspecified phase)
0.6349 Remote Similarity NPD8074 Phase 3
0.6328 Remote Similarity NPD6914 Discontinued
0.632 Remote Similarity NPD8299 Approved
0.632 Remote Similarity NPD8342 Approved
0.632 Remote Similarity NPD8340 Approved
0.632 Remote Similarity NPD8341 Approved
0.6281 Remote Similarity NPD7500 Approved
0.6271 Remote Similarity NPD8413 Clinical (unspecified phase)
0.6261 Remote Similarity NPD6640 Phase 3
0.6154 Remote Similarity NPD8174 Phase 2
0.6142 Remote Similarity NPD8451 Approved
0.6134 Remote Similarity NPD7116 Clinical (unspecified phase)
0.6111 Remote Similarity NPD7829 Approved
0.6111 Remote Similarity NPD7830 Approved
0.6094 Remote Similarity NPD8448 Approved
0.608 Remote Similarity NPD8269 Approved
0.608 Remote Similarity NPD8267 Approved
0.608 Remote Similarity NPD8268 Approved
0.608 Remote Similarity NPD8266 Approved
0.605 Remote Similarity NPD6420 Discontinued
0.6032 Remote Similarity NPD6436 Phase 3
0.6016 Remote Similarity NPD7505 Discontinued
0.5985 Remote Similarity NPD8449 Approved
0.5982 Remote Similarity NPD4228 Discovery
0.597 Remote Similarity NPD8387 Clinical (unspecified phase)
0.5968 Remote Similarity NPD7641 Discontinued
0.5963 Remote Similarity NPD3168 Discontinued
0.5952 Remote Similarity NPD8444 Approved
0.5948 Remote Similarity NPD1407 Approved
0.594 Remote Similarity NPD8450 Suspended
0.5909 Remote Similarity NPD7983 Approved
0.5906 Remote Similarity NPD7623 Phase 3
0.5906 Remote Similarity NPD7624 Clinical (unspecified phase)
0.5896 Remote Similarity NPD8415 Approved
0.5891 Remote Similarity NPD8273 Phase 1
0.5887 Remote Similarity NPD8137 Clinical (unspecified phase)
0.5846 Remote Similarity NPD7747 Phase 1
0.5846 Remote Similarity NPD7746 Phase 1
0.5833 Remote Similarity NPD6413 Approved
0.5827 Remote Similarity NPD8517 Approved
0.5827 Remote Similarity NPD7739 Clinical (unspecified phase)
0.5827 Remote Similarity NPD8513 Phase 3
0.5827 Remote Similarity NPD8516 Approved
0.5827 Remote Similarity NPD8515 Approved
0.5818 Remote Similarity NPD46 Approved
0.5818 Remote Similarity NPD7838 Discovery
0.5818 Remote Similarity NPD6698 Approved
0.5804 Remote Similarity NPD5771 Approved
0.5794 Remote Similarity NPD7522 Discontinued
0.5755 Remote Similarity NPD6695 Phase 3
0.575 Remote Similarity NPD6686 Approved
0.5738 Remote Similarity NPD1719 Phase 1
0.5736 Remote Similarity NPD7642 Approved
0.5714 Remote Similarity NPD5778 Approved
0.5714 Remote Similarity NPD5779 Approved
0.5703 Remote Similarity NPD8274 Clinical (unspecified phase)
0.5702 Remote Similarity NPD8306 Approved
0.5702 Remote Similarity NPD8305 Approved
0.5701 Remote Similarity NPD7338 Clinical (unspecified phase)
0.5688 Remote Similarity NPD7750 Discontinued
0.5659 Remote Similarity NPD8080 Discontinued
0.5645 Remote Similarity NPD3731 Phase 3
0.5625 Remote Similarity NPD8377 Approved
0.5625 Remote Similarity NPD7637 Suspended
0.5625 Remote Similarity NPD8294 Approved
0.562 Remote Similarity NPD6406 Approved
0.5619 Remote Similarity NPD7514 Phase 3
0.5619 Remote Similarity NPD7332 Phase 2
0.5607 Remote Similarity NPD7154 Phase 3
0.56 Remote Similarity NPD3187 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