Structure

Physi-Chem Properties

Molecular Weight:  690.46
Volume:  727.249
LogP:  4.805
LogD:  3.069
LogS:  -4.537
# Rotatable Bonds:  9
TPSA:  142.63
# H-Bond Aceptor:  12
# H-Bond Donor:  1
# Rings:  2
# Heavy Atoms:  12

MedChem Properties

QED Drug-Likeness Score:  0.218
Synthetic Accessibility Score:  5.536
Fsp3:  0.784
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:  -4.946
MDCK Permeability:  1.5011909454187844e-05
Pgp-inhibitor:  0.999
Pgp-substrate:  0.027
Human Intestinal Absorption (HIA):  0.102
20% Bioavailability (F20%):  0.336
30% Bioavailability (F30%):  0.578

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.073
Plasma Protein Binding (PPB):  90.12352752685547%
Volume Distribution (VD):  0.838
Pgp-substrate:  4.657583713531494%

ADMET: Metabolism

CYP1A2-inhibitor:  0.002
CYP1A2-substrate:  0.045
CYP2C19-inhibitor:  0.114
CYP2C19-substrate:  0.723
CYP2C9-inhibitor:  0.077
CYP2C9-substrate:  0.046
CYP2D6-inhibitor:  0.055
CYP2D6-substrate:  0.094
CYP3A4-inhibitor:  0.906
CYP3A4-substrate:  0.77

ADMET: Excretion

Clearance (CL):  7.562
Half-life (T1/2):  0.071

ADMET: Toxicity

hERG Blockers:  0.002
Human Hepatotoxicity (H-HT):  0.992
Drug-inuced Liver Injury (DILI):  0.96
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.026
Maximum Recommended Daily Dose:  0.063
Skin Sensitization:  0.035
Carcinogencity:  0.024
Eye Corrosion:  0.003
Eye Irritation:  0.006
Respiratory Toxicity:  0.048

Download Data

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

  Natural Product: NPC171734

Natural Product ID:  NPC171734
Common Name*:   Veraguamide G
IUPAC Name:   (3S,6S,9S,12S,13R,16S,19S)-3-[(2S)-butan-2-yl]-7,12,17-trimethyl-13-pent-4-enyl-6,9,16-tri(propan-2-yl)-4,14-dioxa-1,7,10,17-tetrazabicyclo[17.3.0]docosane-2,5,8,11,15,18-hexone
Synonyms:   Veraguamide G
Standard InCHIKey:  DUFQJKUNMNJPAD-AVCHBABLSA-N
Standard InCHI:  InChI=1S/C37H62N4O8/c1-13-15-16-19-27-25(10)32(42)38-28(21(3)4)34(44)40(12)30(23(7)8)37(47)49-31(24(9)14-2)35(45)41-20-17-18-26(41)33(43)39(11)29(22(5)6)36(46)48-27/h13,21-31H,1,14-20H2,2-12H3,(H,38,42)/t24-,25-,26-,27+,28-,29-,30-,31-/m0/s1
SMILES:  C=CCCC[C@@H]1[C@H](C)C(=N[C@@H](C(C)C)C(=O)N(C)[C@@H](C(C)C)C(=O)O[C@@H]([C@@H](C)CC)C(=O)N2CCC[C@H]2C(=O)N(C)[C@@H](C(C)C)C(=O)O1)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL1783473
PubChem CID:   53355453
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
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. PMID[11975485]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. PMID[21446699]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. PMID[31763840]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria n.a. n.a. n.a. PMID[9748368]
NPO16362 Symploca hydnoides Species Microcoleaceae Bacteria 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
NPT139 Cell Line HT-29 Homo sapiens IC50 = 2700.0 nM PMID[492362]
NPT165 Cell Line HeLa Homo sapiens IC50 = 2300.0 nM PMID[492362]

☑ 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 NPC171734 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
0.9 High Similarity NPC220234
0.8738 High Similarity NPC301148
0.8738 High Similarity NPC124554
0.8738 High Similarity NPC5864
0.8571 High Similarity NPC124549
0.8558 High Similarity NPC471097
0.8558 High Similarity NPC475149
0.8476 Intermediate Similarity NPC198344
0.8365 Intermediate Similarity NPC13175
0.8365 Intermediate Similarity NPC475791
0.8333 Intermediate Similarity NPC67009
0.8269 Intermediate Similarity NPC475758
0.7946 Intermediate Similarity NPC476875
0.7864 Intermediate Similarity NPC173763
0.7864 Intermediate Similarity NPC471098
0.7864 Intermediate Similarity NPC62263
0.7767 Intermediate Similarity NPC474576
0.7727 Intermediate Similarity NPC323720
0.767 Intermediate Similarity NPC474593
0.767 Intermediate Similarity NPC475801
0.7636 Intermediate Similarity NPC476877
0.7586 Intermediate Similarity NPC103391
0.7586 Intermediate Similarity NPC472536
0.75 Intermediate Similarity NPC476876
0.75 Intermediate Similarity NPC315188
0.7431 Intermediate Similarity NPC475440
0.7368 Intermediate Similarity NPC207820
0.7348 Intermediate Similarity NPC269398
0.7348 Intermediate Similarity NPC263493
0.7333 Intermediate Similarity NPC225648
0.7333 Intermediate Similarity NPC329761
0.7313 Intermediate Similarity NPC5620
0.7258 Intermediate Similarity NPC309525
0.7193 Intermediate Similarity NPC475637
0.7121 Intermediate Similarity NPC471265
0.7121 Intermediate Similarity NPC471264
0.7105 Intermediate Similarity NPC205176
0.7103 Intermediate Similarity NPC476019
0.7101 Intermediate Similarity NPC129666
0.708 Intermediate Similarity NPC145113
0.7037 Intermediate Similarity NPC161069
0.7 Intermediate Similarity NPC477145
0.7 Intermediate Similarity NPC473741
0.6992 Remote Similarity NPC68865
0.6991 Remote Similarity NPC188785
0.6977 Remote Similarity NPC120335
0.694 Remote Similarity NPC98424
0.694 Remote Similarity NPC476133
0.694 Remote Similarity NPC470884
0.694 Remote Similarity NPC178662
0.694 Remote Similarity NPC92784
0.6937 Remote Similarity NPC47076
0.6937 Remote Similarity NPC134504
0.6934 Remote Similarity NPC209509
0.6916 Remote Similarity NPC322966
0.6912 Remote Similarity NPC139326
0.6906 Remote Similarity NPC240848
0.6893 Remote Similarity NPC246005
0.6881 Remote Similarity NPC315237
0.688 Remote Similarity NPC273185
0.6879 Remote Similarity NPC162104
0.6875 Remote Similarity NPC297145
0.6875 Remote Similarity NPC197743
0.6861 Remote Similarity NPC476978
0.6855 Remote Similarity NPC470652
0.6835 Remote Similarity NPC138775
0.68 Remote Similarity NPC477238
0.6789 Remote Similarity NPC477538
0.6786 Remote Similarity NPC471820
0.6786 Remote Similarity NPC471821
0.6786 Remote Similarity NPC473597
0.6777 Remote Similarity NPC63191
0.6777 Remote Similarity NPC471202
0.6772 Remote Similarity NPC470654
0.6772 Remote Similarity NPC470653
0.6772 Remote Similarity NPC470650
0.6768 Remote Similarity NPC263281
0.6768 Remote Similarity NPC178919
0.6765 Remote Similarity NPC163392
0.6765 Remote Similarity NPC239762
0.6738 Remote Similarity NPC2501
0.6731 Remote Similarity NPC84128
0.6731 Remote Similarity NPC53858
0.67 Remote Similarity NPC86064
0.6696 Remote Similarity NPC469739
0.6667 Remote Similarity NPC296043
0.6642 Remote Similarity NPC268841
0.6642 Remote Similarity NPC307357
0.6642 Remote Similarity NPC46098
0.664 Remote Similarity NPC477237
0.6635 Remote Similarity NPC476302
0.6618 Remote Similarity NPC127741
0.6613 Remote Similarity NPC329216
0.66 Remote Similarity NPC43219
0.6597 Remote Similarity NPC122590
0.6571 Remote Similarity NPC316008
0.6571 Remote Similarity NPC313867
0.6538 Remote Similarity NPC476156
0.6538 Remote Similarity NPC476117
0.6538 Remote Similarity NPC476243
0.6538 Remote Similarity NPC476137
0.6535 Remote Similarity NPC160688
0.6525 Remote Similarity NPC314358
0.6504 Remote Similarity NPC469597
0.65 Remote Similarity NPC52748
0.65 Remote Similarity NPC315283
0.65 Remote Similarity NPC314388
0.6493 Remote Similarity NPC130309
0.6489 Remote Similarity NPC470655
0.6489 Remote Similarity NPC470651
0.6471 Remote Similarity NPC241394
0.6465 Remote Similarity NPC478256
0.6449 Remote Similarity NPC472351
0.6442 Remote Similarity NPC31756
0.6434 Remote Similarity NPC105717
0.6417 Remote Similarity NPC271562
0.6415 Remote Similarity NPC284456
0.6415 Remote Similarity NPC6902
0.6408 Remote Similarity NPC262077
0.6389 Remote Similarity NPC227051
0.6387 Remote Similarity NPC128303
0.6378 Remote Similarity NPC469899
0.6372 Remote Similarity NPC38172
0.6364 Remote Similarity NPC212866
0.6364 Remote Similarity NPC135121
0.6364 Remote Similarity NPC15413
0.6364 Remote Similarity NPC29598
0.6364 Remote Similarity NPC473495
0.6357 Remote Similarity NPC469427
0.6357 Remote Similarity NPC469426
0.6357 Remote Similarity NPC168113
0.6355 Remote Similarity NPC474312
0.635 Remote Similarity NPC248283
0.6345 Remote Similarity NPC7817
0.6345 Remote Similarity NPC475168
0.6341 Remote Similarity NPC474411
0.6341 Remote Similarity NPC474431
0.6339 Remote Similarity NPC17143
0.6339 Remote Similarity NPC47230
0.6336 Remote Similarity NPC46427
0.6336 Remote Similarity NPC6975
0.6325 Remote Similarity NPC233932
0.6324 Remote Similarity NPC99864
0.6312 Remote Similarity NPC176226
0.6312 Remote Similarity NPC197682
0.6308 Remote Similarity NPC50520
0.6306 Remote Similarity NPC155230
0.6303 Remote Similarity NPC265094
0.6296 Remote Similarity NPC95478
0.6296 Remote Similarity NPC145748
0.6296 Remote Similarity NPC155670
0.627 Remote Similarity NPC473819
0.6269 Remote Similarity NPC319766
0.6263 Remote Similarity NPC10716
0.6262 Remote Similarity NPC184473
0.626 Remote Similarity NPC251122
0.626 Remote Similarity NPC252878
0.6259 Remote Similarity NPC473341
0.6259 Remote Similarity NPC286551
0.625 Remote Similarity NPC120420
0.625 Remote Similarity NPC477729
0.6242 Remote Similarity NPC317362
0.6242 Remote Similarity NPC318930
0.6224 Remote Similarity NPC201244
0.6224 Remote Similarity NPC477217
0.6224 Remote Similarity NPC315266
0.6216 Remote Similarity NPC470902
0.6216 Remote Similarity NPC324506
0.6209 Remote Similarity NPC472923
0.6204 Remote Similarity NPC246079
0.62 Remote Similarity NPC474812
0.619 Remote Similarity NPC315809
0.619 Remote Similarity NPC471645
0.619 Remote Similarity NPC314050
0.6183 Remote Similarity NPC202521
0.6182 Remote Similarity NPC477539
0.617 Remote Similarity NPC476259
0.6168 Remote Similarity NPC470783
0.6168 Remote Similarity NPC23984
0.6161 Remote Similarity NPC275715
0.6159 Remote Similarity NPC287401
0.6148 Remote Similarity NPC313657
0.6139 Remote Similarity NPC317725
0.6139 Remote Similarity NPC326407
0.6132 Remote Similarity NPC478017
0.6132 Remote Similarity NPC315535
0.6132 Remote Similarity NPC315131
0.6125 Remote Similarity NPC475421
0.6107 Remote Similarity NPC476990
0.6103 Remote Similarity NPC473322
0.6094 Remote Similarity NPC209734
0.609 Remote Similarity NPC474371
0.6084 Remote Similarity NPC142761
0.6077 Remote Similarity NPC310467
0.6066 Remote Similarity NPC475918
0.6063 Remote Similarity NPC474984
0.6053 Remote Similarity NPC1390
0.6053 Remote Similarity NPC62104
0.6051 Remote Similarity NPC475123
0.6051 Remote Similarity NPC475204

  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 NPC171734 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
0.6792 Remote Similarity NPD3723 Clinical (unspecified phase)
0.6789 Remote Similarity NPD4780 Clinical (unspecified phase)
0.6636 Remote Similarity NPD7760 Phase 2
0.6636 Remote Similarity NPD7759 Phase 2
0.6579 Remote Similarity NPD3713 Approved
0.6579 Remote Similarity NPD3714 Approved
0.6579 Remote Similarity NPD3715 Approved
0.6518 Remote Similarity NPD5781 Clinical (unspecified phase)
0.6496 Remote Similarity NPD8173 Phase 2
0.6496 Remote Similarity NPD8172 Phase 2
0.6486 Remote Similarity NPD4261 Phase 1
0.6476 Remote Similarity NPD7762 Phase 2
0.6476 Remote Similarity NPD7763 Phase 2
0.6435 Remote Similarity NPD8038 Phase 2
0.6404 Remote Similarity NPD7841 Clinical (unspecified phase)
0.6364 Remote Similarity NPD7840 Approved
0.6324 Remote Similarity NPD8415 Approved
0.6304 Remote Similarity NPD7113 Clinical (unspecified phase)
0.6262 Remote Similarity NPD2683 Discontinued
0.6167 Remote Similarity NPD6122 Discontinued
0.6159 Remote Similarity NPD8387 Clinical (unspecified phase)
0.6132 Remote Similarity NPD7917 Clinical (unspecified phase)
0.6132 Remote Similarity NPD7918 Clinical (unspecified phase)
0.6129 Remote Similarity NPD6421 Discontinued
0.609 Remote Similarity NPD2584 Suspended
0.6074 Remote Similarity NPD2585 Clinical (unspecified phase)
0.6071 Remote Similarity NPD3177 Phase 3
0.6067 Remote Similarity NPD8414 Discontinued
0.6053 Remote Similarity NPD2682 Approved
0.6 Remote Similarity NPD8416 Discontinued
0.5985 Remote Similarity NPD4175 Approved
0.5985 Remote Similarity NPD4177 Approved
0.5984 Remote Similarity NPD8298 Phase 2
0.597 Remote Similarity NPD8273 Phase 1
0.5952 Remote Similarity NPD2204 Approved
0.5944 Remote Similarity NPD8384 Approved
0.592 Remote Similarity NPD6413 Approved
0.5918 Remote Similarity NPD8323 Discontinued
0.5915 Remote Similarity NPD6073 Approved
0.5915 Remote Similarity NPD5725 Approved
0.5887 Remote Similarity NPD2147 Approved
0.5862 Remote Similarity NPD6699 Clinical (unspecified phase)
0.5845 Remote Similarity NPD8643 Discontinued
0.5833 Remote Similarity NPD4825 Clinical (unspecified phase)
0.5825 Remote Similarity NPD2694 Approved
0.5825 Remote Similarity NPD2696 Approved
0.5825 Remote Similarity NPD2697 Approved
0.5825 Remote Similarity NPD2695 Approved
0.5818 Remote Similarity NPD1125 Discovery
0.5816 Remote Similarity NPD5747 Discontinued
0.5814 Remote Similarity NPD7915 Approved
0.5814 Remote Similarity NPD7916 Approved
0.5809 Remote Similarity NPD7746 Phase 1
0.5809 Remote Similarity NPD7747 Phase 1
0.5798 Remote Similarity NPD5349 Clinical (unspecified phase)
0.5798 Remote Similarity NPD1784 Approved
0.5798 Remote Similarity NPD4228 Discovery
0.5797 Remote Similarity NPD7751 Phase 1
0.5728 Remote Similarity NPD620 Approved
0.5728 Remote Similarity NPD3724 Clinical (unspecified phase)
0.5724 Remote Similarity NPD6077 Discontinued
0.5714 Remote Similarity NPD8417 Discontinued
0.5714 Remote Similarity NPD7979 Clinical (unspecified phase)
0.5704 Remote Similarity NPD7634 Clinical (unspecified phase)
0.5683 Remote Similarity NPD3608 Clinical (unspecified phase)
0.5682 Remote Similarity NPD7756 Clinical (unspecified phase)
0.5664 Remote Similarity NPD8265 Approved
0.5664 Remote Similarity NPD4153 Approved
0.5656 Remote Similarity NPD5359 Clinical (unspecified phase)
0.5655 Remote Similarity NPD6852 Discontinued
0.5646 Remote Similarity NPD8076 Discontinued
0.5641 Remote Similarity NPD6095 Approved
0.5641 Remote Similarity NPD6094 Approved
0.5635 Remote Similarity NPD6937 Approved
0.563 Remote Similarity NPD7652 Discontinued
0.5625 Remote Similarity NPD5767 Discontinued
0.5625 Remote Similarity NPD6420 Discontinued
0.562 Remote Similarity NPD3072 Approved
0.562 Remote Similarity NPD3073 Approved
0.562 Remote Similarity NPD3071 Approved
0.5615 Remote Similarity NPD1376 Discontinued
0.5608 Remote Similarity NPD6681 Discovery
0.5606 Remote Similarity NPD961 Discontinued
0.5605 Remote Similarity NPD4557 Approved
0.5603 Remote Similarity NPD4125 Approved
0.56 Remote Similarity NPD2054 Approved
0.56 Remote Similarity NPD2055 Phase 3

  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