Structure

Physi-Chem Properties

Molecular Weight:  551.33
Volume:  559.132
LogP:  1.725
LogD:  1.64
LogS:  -3.022
# Rotatable Bonds:  4
TPSA:  154.22
# H-Bond Aceptor:  12
# H-Bond Donor:  3
# Rings:  2
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.426
Synthetic Accessibility Score:  4.882
Fsp3:  0.778
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:  -5.438
MDCK Permeability:  4.396590156829916e-05
Pgp-inhibitor:  0.989
Pgp-substrate:  0.991
Human Intestinal Absorption (HIA):  0.123
20% Bioavailability (F20%):  0.012
30% Bioavailability (F30%):  0.407

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.194
Plasma Protein Binding (PPB):  63.576202392578125%
Volume Distribution (VD):  0.47
Pgp-substrate:  49.1129150390625%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.04
CYP2C19-inhibitor:  0.066
CYP2C19-substrate:  0.1
CYP2C9-inhibitor:  0.073
CYP2C9-substrate:  0.144
CYP2D6-inhibitor:  0.007
CYP2D6-substrate:  0.096
CYP3A4-inhibitor:  0.455
CYP3A4-substrate:  0.257

ADMET: Excretion

Clearance (CL):  4.49
Half-life (T1/2):  0.81

ADMET: Toxicity

hERG Blockers:  0.004
Human Hepatotoxicity (H-HT):  0.886
Drug-inuced Liver Injury (DILI):  0.808
AMES Toxicity:  0.006
Rat Oral Acute Toxicity:  0.594
Maximum Recommended Daily Dose:  0.165
Skin Sensitization:  0.072
Carcinogencity:  0.022
Eye Corrosion:  0.003
Eye Irritation:  0.005
Respiratory Toxicity:  0.011

Download Data

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

  Natural Product: NPC475801

Natural Product ID:  NPC475801
Common Name*:   Desmethyldestruxin B2
IUPAC Name:   (3R,10S,13S,16S,19S)-16-ethyl-10,11-dimethyl-3-(2-methylpropyl)-13-propan-2-yl-4-oxa-1,8,11,14,17-pentazabicyclo[17.3.0]docosane-2,5,9,12,15,18-hexone
Synonyms:   Desmethyldestruxin B2
Standard InCHIKey:  DXGREKPJNZCYLD-UERWRGBPSA-N
Standard InCHI:  InChI=1S/C27H45N5O7/c1-8-18-24(35)30-22(16(4)5)27(38)31(7)17(6)23(34)28-12-11-21(33)39-20(14-15(2)3)26(37)32-13-9-10-19(32)25(36)29-18/h15-20,22H,8-14H2,1-7H3,(H,28,34)(H,29,36)(H,30,35)/t17-,18-,19-,20+,22-/m0/s1
SMILES:  CCC1C(=O)NC(C(=O)N(C(C(=O)NCCC(=O)OC(C(=O)N2CCCC2C(=O)N1)CC(C)C)C)C)C(C)C
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL516354
PubChem CID:   44575684
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0000264] Organic acids and derivatives
      • [CHEMONTID:0001813] Peptidomimetics
        • [CHEMONTID:0001961] Depsipeptides
          • [CHEMONTID:0001994] Cyclic depsipeptides

*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
NPO9967 Metarhizium anisopliae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[10650095]
NPO9967 Metarhizium anisopliae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[18044842]
NPO9967 Metarhizium anisopliae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[20233596]
NPO9967 Metarhizium anisopliae Species Clavicipitaceae Eukaryota n.a. n.a. n.a. PMID[7623030]
NPO9967 Metarhizium anisopliae Species Clavicipitaceae 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
NPT963 Organism Hepatitis B virus Hepatitis B virus IC50 = 1.5 ug.mL-1 PMID[542510]

☑ 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 NPC475801 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 NPC474593
0.9881 High Similarity NPC474576
0.9765 High Similarity NPC62263
0.9765 High Similarity NPC173763
0.9765 High Similarity NPC471098
0.8913 High Similarity NPC475440
0.871 High Similarity NPC475758
0.8632 High Similarity NPC471097
0.8632 High Similarity NPC475149
0.8617 High Similarity NPC475791
0.8617 High Similarity NPC13175
0.8367 Intermediate Similarity NPC475637
0.8316 Intermediate Similarity NPC220234
0.8081 Intermediate Similarity NPC323720
0.8061 Intermediate Similarity NPC5864
0.8061 Intermediate Similarity NPC301148
0.8061 Intermediate Similarity NPC124554
0.798 Intermediate Similarity NPC198344
0.7957 Intermediate Similarity NPC477538
0.7917 Intermediate Similarity NPC473597
0.79 Intermediate Similarity NPC124549
0.7841 Intermediate Similarity NPC470783
0.767 Intermediate Similarity NPC67009
0.767 Intermediate Similarity NPC171734
0.7614 Intermediate Similarity NPC31756
0.7579 Intermediate Similarity NPC476019
0.7556 Intermediate Similarity NPC246005
0.7528 Intermediate Similarity NPC476117
0.7528 Intermediate Similarity NPC476243
0.7528 Intermediate Similarity NPC476156
0.7528 Intermediate Similarity NPC476137
0.7444 Intermediate Similarity NPC475542
0.7444 Intermediate Similarity NPC476302
0.7442 Intermediate Similarity NPC161774
0.7442 Intermediate Similarity NPC263281
0.7442 Intermediate Similarity NPC256312
0.7442 Intermediate Similarity NPC266888
0.7416 Intermediate Similarity NPC312315
0.7315 Intermediate Similarity NPC471202
0.7315 Intermediate Similarity NPC63191
0.7241 Intermediate Similarity NPC209156
0.7241 Intermediate Similarity NPC178919
0.7234 Intermediate Similarity NPC477539
0.7209 Intermediate Similarity NPC214532
0.7209 Intermediate Similarity NPC196007
0.7209 Intermediate Similarity NPC76297
0.7188 Intermediate Similarity NPC322966
0.7174 Intermediate Similarity NPC84128
0.7174 Intermediate Similarity NPC53858
0.713 Intermediate Similarity NPC476875
0.7111 Intermediate Similarity NPC473741
0.7111 Intermediate Similarity NPC477145
0.7059 Intermediate Similarity NPC10716
0.7045 Intermediate Similarity NPC126186
0.703 Intermediate Similarity NPC134504
0.703 Intermediate Similarity NPC47076
0.701 Intermediate Similarity NPC275715
0.7 Intermediate Similarity NPC59867
0.6977 Remote Similarity NPC29598
0.6977 Remote Similarity NPC212866
0.697 Remote Similarity NPC315237
0.6966 Remote Similarity NPC327272
0.6897 Remote Similarity NPC478256
0.6889 Remote Similarity NPC470782
0.6887 Remote Similarity NPC128303
0.6822 Remote Similarity NPC241394
0.6792 Remote Similarity NPC476877
0.6667 Remote Similarity NPC476876
0.6629 Remote Similarity NPC470781
0.6628 Remote Similarity NPC84182
0.6628 Remote Similarity NPC128005
0.6604 Remote Similarity NPC188785
0.6581 Remote Similarity NPC477238
0.6581 Remote Similarity NPC315188
0.6552 Remote Similarity NPC469899
0.6535 Remote Similarity NPC471264
0.6535 Remote Similarity NPC471265
0.6517 Remote Similarity NPC476285
0.6495 Remote Similarity NPC145748
0.6495 Remote Similarity NPC155670
0.6495 Remote Similarity NPC95478
0.6495 Remote Similarity NPC472351
0.6484 Remote Similarity NPC98424
0.6484 Remote Similarity NPC470884
0.6484 Remote Similarity NPC178662
0.6484 Remote Similarity NPC476133
0.6484 Remote Similarity NPC43219
0.6484 Remote Similarity NPC138435
0.6484 Remote Similarity NPC92784
0.6458 Remote Similarity NPC184473
0.6429 Remote Similarity NPC227051
0.6413 Remote Similarity NPC86064
0.641 Remote Similarity NPC477237
0.6404 Remote Similarity NPC322274
0.6392 Remote Similarity NPC235078
0.6374 Remote Similarity NPC141325
0.6354 Remote Similarity NPC23984
0.6348 Remote Similarity NPC103391
0.6348 Remote Similarity NPC472536
0.6344 Remote Similarity NPC476324
0.6344 Remote Similarity NPC476130
0.6333 Remote Similarity NPC476291
0.6289 Remote Similarity NPC6902
0.6286 Remote Similarity NPC117829
0.6279 Remote Similarity NPC243964
0.625 Remote Similarity NPC207820
0.625 Remote Similarity NPC287693
0.6241 Remote Similarity NPC209509
0.6238 Remote Similarity NPC52533
0.6222 Remote Similarity NPC193280
0.6222 Remote Similarity NPC314273
0.6218 Remote Similarity NPC470652
0.6211 Remote Similarity NPC233108
0.6207 Remote Similarity NPC57420
0.6154 Remote Similarity NPC296043
0.6148 Remote Similarity NPC470653
0.6148 Remote Similarity NPC470654
0.6148 Remote Similarity NPC470650
0.6136 Remote Similarity NPC263493
0.6136 Remote Similarity NPC269398
0.6136 Remote Similarity NPC128559
0.6136 Remote Similarity NPC160661
0.6129 Remote Similarity NPC320221
0.6129 Remote Similarity NPC476248
0.6126 Remote Similarity NPC205176
0.6122 Remote Similarity NPC284456
0.6111 Remote Similarity NPC306696
0.6105 Remote Similarity NPC472594
0.6103 Remote Similarity NPC240848
0.6102 Remote Similarity NPC329216
0.6098 Remote Similarity NPC309525
0.6095 Remote Similarity NPC301010
0.6078 Remote Similarity NPC473495
0.6038 Remote Similarity NPC280066
0.6033 Remote Similarity NPC160688
0.602 Remote Similarity NPC314466
0.6019 Remote Similarity NPC155230
0.6 Remote Similarity NPC5620
0.5981 Remote Similarity NPC469739
0.5965 Remote Similarity NPC296143
0.5962 Remote Similarity NPC477729
0.593 Remote Similarity NPC473599
0.5909 Remote Similarity NPC105297
0.5895 Remote Similarity NPC472595
0.5887 Remote Similarity NPC477518
0.5882 Remote Similarity NPC473819
0.5876 Remote Similarity NPC37681
0.5876 Remote Similarity NPC316242
0.5876 Remote Similarity NPC325902
0.5873 Remote Similarity NPC470655
0.5873 Remote Similarity NPC470651
0.587 Remote Similarity NPC471820
0.587 Remote Similarity NPC471821
0.5857 Remote Similarity NPC162104
0.5854 Remote Similarity NPC273185
0.5851 Remote Similarity NPC477643
0.5851 Remote Similarity NPC29326
0.5851 Remote Similarity NPC320865
0.5851 Remote Similarity NPC477641
0.5843 Remote Similarity NPC145658
0.5827 Remote Similarity NPC129666
0.5825 Remote Similarity NPC477728
0.5816 Remote Similarity NPC315535
0.5816 Remote Similarity NPC315131
0.5816 Remote Similarity NPC478017
0.5806 Remote Similarity NPC50520
0.5806 Remote Similarity NPC477642
0.5795 Remote Similarity NPC477644
0.5795 Remote Similarity NPC314510
0.5794 Remote Similarity NPC38172
0.5784 Remote Similarity NPC277918
0.578 Remote Similarity NPC313821
0.5769 Remote Similarity NPC324506
0.5747 Remote Similarity NPC321468
0.5747 Remote Similarity NPC327748
0.5736 Remote Similarity NPC120335
0.5735 Remote Similarity NPC139326
0.5726 Remote Similarity NPC251122
0.5714 Remote Similarity NPC191774
0.5701 Remote Similarity NPC208537
0.5701 Remote Similarity NPC270005
0.5699 Remote Similarity NPC473985
0.5699 Remote Similarity NPC28348
0.5699 Remote Similarity NPC475808
0.5699 Remote Similarity NPC474299
0.5699 Remote Similarity NPC474298
0.5699 Remote Similarity NPC472579
0.5698 Remote Similarity NPC317147
0.5693 Remote Similarity NPC476978
0.5683 Remote Similarity NPC225648
0.5683 Remote Similarity NPC329761
0.5682 Remote Similarity NPC327170
0.5682 Remote Similarity NPC329564
0.5676 Remote Similarity NPC475188
0.5672 Remote Similarity NPC68865
0.5667 Remote Similarity NPC259586
0.5663 Remote Similarity NPC322946
0.5659 Remote Similarity NPC313657
0.5655 Remote Similarity NPC297145
0.5655 Remote Similarity NPC197743

  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 NPC475801 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
0.7802 Intermediate Similarity NPD7759 Phase 2
0.7802 Intermediate Similarity NPD7760 Phase 2
0.7579 Intermediate Similarity NPD4780 Clinical (unspecified phase)
0.7444 Intermediate Similarity NPD7763 Phase 2
0.7444 Intermediate Similarity NPD7762 Phase 2
0.7396 Intermediate Similarity NPD4261 Phase 1
0.7363 Intermediate Similarity NPD2683 Discontinued
0.73 Intermediate Similarity NPD8038 Phase 2
0.7282 Intermediate Similarity NPD6122 Discontinued
0.7234 Intermediate Similarity NPD3723 Clinical (unspecified phase)
0.7174 Intermediate Similarity NPD1125 Discovery
0.71 Intermediate Similarity NPD7841 Clinical (unspecified phase)
0.7083 Intermediate Similarity NPD3177 Phase 3
0.6977 Remote Similarity NPD7840 Approved
0.6796 Remote Similarity NPD3715 Approved
0.6796 Remote Similarity NPD3713 Approved
0.6796 Remote Similarity NPD3714 Approved
0.6404 Remote Similarity NPD620 Approved
0.6355 Remote Similarity NPD6120 Clinical (unspecified phase)
0.6333 Remote Similarity NPD2220 Clinical (unspecified phase)
0.6327 Remote Similarity NPD3733 Clinical (unspecified phase)
0.6327 Remote Similarity NPD9577 Approved
0.6316 Remote Similarity NPD4815 Discontinued
0.6311 Remote Similarity NPD6699 Clinical (unspecified phase)
0.6306 Remote Similarity NPD6937 Approved
0.6277 Remote Similarity NPD2689 Clinical (unspecified phase)
0.6222 Remote Similarity NPD3724 Clinical (unspecified phase)
0.6214 Remote Similarity NPD2682 Approved
0.62 Remote Similarity NPD5791 Phase 2
0.617 Remote Similarity NPD1453 Phase 1
0.6154 Remote Similarity NPD2697 Approved
0.6154 Remote Similarity NPD2696 Approved
0.6154 Remote Similarity NPD9649 Approved
0.6154 Remote Similarity NPD2695 Approved
0.6154 Remote Similarity NPD2694 Approved
0.6111 Remote Similarity NPD322 Phase 1
0.6068 Remote Similarity NPD7915 Approved
0.6068 Remote Similarity NPD7916 Approved
0.6058 Remote Similarity NPD5792 Clinical (unspecified phase)
0.598 Remote Similarity NPD3176 Clinical (unspecified phase)
0.5963 Remote Similarity NPD4825 Clinical (unspecified phase)
0.5952 Remote Similarity NPD1456 Approved
0.5929 Remote Similarity NPD1385 Discontinued
0.5926 Remote Similarity NPD1784 Approved
0.59 Remote Similarity NPD4829 Discontinued
0.5854 Remote Similarity NPD7652 Discontinued
0.5851 Remote Similarity NPD2256 Clinical (unspecified phase)
0.5816 Remote Similarity NPD7917 Clinical (unspecified phase)
0.5816 Remote Similarity NPD7918 Clinical (unspecified phase)
0.578 Remote Similarity NPD3190 Approved
0.578 Remote Similarity NPD3191 Approved
0.578 Remote Similarity NPD3189 Approved
0.5758 Remote Similarity NPD9578 Clinical (unspecified phase)
0.5743 Remote Similarity NPD883 Phase 2
0.5743 Remote Similarity NPD882 Phase 2
0.5726 Remote Similarity NPD1805 Phase 2
0.5726 Remote Similarity NPD1804 Phase 2
0.5714 Remote Similarity NPD4278 Clinical (unspecified phase)
0.5714 Remote Similarity NPD9419 Clinical (unspecified phase)
0.5714 Remote Similarity NPD3160 Suspended
0.5698 Remote Similarity NPD9425 Approved
0.5688 Remote Similarity NPD7844 Discontinued
0.5663 Remote Similarity NPD9441 Phase 2
0.5652 Remote Similarity NPD1428 Phase 2
0.5652 Remote Similarity NPD2263 Discontinued
0.5647 Remote Similarity NPD4276 Approved
0.5647 Remote Similarity NPD4277 Approved
0.5644 Remote Similarity NPD1448 Clinical (unspecified phase)
0.5638 Remote Similarity NPD1439 Clinical (unspecified phase)
0.5625 Remote Similarity NPD5359 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