Structure

Physi-Chem Properties

Molecular Weight:  370.15
Volume:  343.22
LogP:  -2.514
LogD:  -1.756
LogS:  -1.631
# Rotatable Bonds:  4
TPSA:  165.14
# H-Bond Aceptor:  11
# H-Bond Donor:  5
# Rings:  2
# Heavy Atoms:  11

MedChem Properties

QED Drug-Likeness Score:  0.35
Synthetic Accessibility Score:  4.09
Fsp3:  0.667
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  0
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.766
MDCK Permeability:  9.744573617354035e-05
Pgp-inhibitor:  0.012
Pgp-substrate:  0.397
Human Intestinal Absorption (HIA):  0.985
20% Bioavailability (F20%):  0.998
30% Bioavailability (F30%):  0.99

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.351
Plasma Protein Binding (PPB):  9.17768669128418%
Volume Distribution (VD):  0.262
Pgp-substrate:  84.88773345947266%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.022
CYP2C19-inhibitor:  0.028
CYP2C19-substrate:  0.039
CYP2C9-inhibitor:  0.047
CYP2C9-substrate:  0.755
CYP2D6-inhibitor:  0.001
CYP2D6-substrate:  0.101
CYP3A4-inhibitor:  0.003
CYP3A4-substrate:  0.003

ADMET: Excretion

Clearance (CL):  1.825
Half-life (T1/2):  0.856

ADMET: Toxicity

hERG Blockers:  0.005
Human Hepatotoxicity (H-HT):  0.161
Drug-inuced Liver Injury (DILI):  0.026
AMES Toxicity:  0.008
Rat Oral Acute Toxicity:  0.018
Maximum Recommended Daily Dose:  0.012
Skin Sensitization:  0.155
Carcinogencity:  0.008
Eye Corrosion:  0.003
Eye Irritation:  0.009
Respiratory Toxicity:  0.015

Download Data

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

  Natural Product: NPC475542

Natural Product ID:  NPC475542
Common Name*:   Cyclo-(Glycyl-L-Seryl-L-Prolyl-L-Glutamyl)
IUPAC Name:   3-[(3S,9S,12S)-3-(hydroxymethyl)-2,5,8,11-tetraoxo-1,4,7,10-tetrazabicyclo[10.3.0]pentadecan-9-yl]propanoic acid
Synonyms:  
Standard InCHIKey:  HCPCZMCZJYSIAJ-GUBZILKMSA-N
Standard InCHI:  InChI=1S/C15H22N4O7/c20-7-9-15(26)19-5-1-2-10(19)14(25)18-8(3-4-12(22)23)13(24)16-6-11(21)17-9/h8-10,20H,1-7H2,(H,16,24)(H,17,21)(H,18,25)(H,22,23)/t8-,9-,10-/m0/s1
SMILES:  C1CC2C(=O)NC(C(=O)NCC(=O)NC(C(=O)N2C1)CO)CCC(=O)O
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL507856
PubChem CID:   11360698
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:0000348] Peptides
            • [CHEMONTID:0004831] Oligopeptides

*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
NPO20897.1 Suberites domuncula Under-species n.a. n.a. n.a. n.a. n.a. PMID[15270577]

☑ 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
NPT22 Organism Bacillus subtilis subsp. spizizenii Bacillus subtilis subsp. spizizenii MIC = 25.0 ug.mL-1 PMID[575647]

☑ 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 NPC475542 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
0.8701 High Similarity NPC59867
0.8052 Intermediate Similarity NPC470781
0.7875 Intermediate Similarity NPC470782
0.7805 Intermediate Similarity NPC312315
0.7444 Intermediate Similarity NPC475801
0.7444 Intermediate Similarity NPC474593
0.7412 Intermediate Similarity NPC470783
0.7407 Intermediate Similarity NPC126186
0.7381 Intermediate Similarity NPC31756
0.7363 Intermediate Similarity NPC474576
0.7294 Intermediate Similarity NPC476156
0.7294 Intermediate Similarity NPC476117
0.7294 Intermediate Similarity NPC476243
0.7294 Intermediate Similarity NPC476137
0.7283 Intermediate Similarity NPC173763
0.7283 Intermediate Similarity NPC62263
0.7283 Intermediate Similarity NPC471098
0.7209 Intermediate Similarity NPC476302
0.7195 Intermediate Similarity NPC256312
0.7195 Intermediate Similarity NPC266888
0.7195 Intermediate Similarity NPC209156
0.7195 Intermediate Similarity NPC161774
0.7188 Intermediate Similarity NPC475440
0.7179 Intermediate Similarity NPC84182
0.7179 Intermediate Similarity NPC128005
0.716 Intermediate Similarity NPC76297
0.716 Intermediate Similarity NPC196007
0.716 Intermediate Similarity NPC214532
0.7158 Intermediate Similarity NPC473597
0.7013 Intermediate Similarity NPC243964
0.6962 Remote Similarity NPC287693
0.6957 Remote Similarity NPC275715
0.6932 Remote Similarity NPC53858
0.6932 Remote Similarity NPC84128
0.6914 Remote Similarity NPC322274
0.6813 Remote Similarity NPC477539
0.6809 Remote Similarity NPC477538
0.6786 Remote Similarity NPC320221
0.6765 Remote Similarity NPC475637
0.6706 Remote Similarity NPC327272
0.6667 Remote Similarity NPC475758
0.6634 Remote Similarity NPC475149
0.6634 Remote Similarity NPC471097
0.6633 Remote Similarity NPC134504
0.6633 Remote Similarity NPC47076
0.66 Remote Similarity NPC13175
0.66 Remote Similarity NPC475791
0.6505 Remote Similarity NPC323720
0.6505 Remote Similarity NPC128303
0.65 Remote Similarity NPC57420
0.6471 Remote Similarity NPC29326
0.6449 Remote Similarity NPC476875
0.6442 Remote Similarity NPC241394
0.642 Remote Similarity NPC160661
0.641 Remote Similarity NPC321536
0.6408 Remote Similarity NPC476877
0.6375 Remote Similarity NPC327252
0.6337 Remote Similarity NPC220234
0.633 Remote Similarity NPC63191
0.633 Remote Similarity NPC471202
0.6329 Remote Similarity NPC143722
0.6321 Remote Similarity NPC67009
0.6286 Remote Similarity NPC476876
0.625 Remote Similarity NPC322966
0.62 Remote Similarity NPC117829
0.6154 Remote Similarity NPC301148
0.6154 Remote Similarity NPC5864
0.6154 Remote Similarity NPC124554
0.6104 Remote Similarity NPC322573
0.6095 Remote Similarity NPC198344
0.6061 Remote Similarity NPC315237
0.6053 Remote Similarity NPC263065
0.6053 Remote Similarity NPC189178
0.6038 Remote Similarity NPC124549
0.6026 Remote Similarity NPC325985
0.6022 Remote Similarity NPC184473
0.6 Remote Similarity NPC329077
0.5929 Remote Similarity NPC296043
0.5921 Remote Similarity NPC29950
0.5921 Remote Similarity NPC19576
0.5913 Remote Similarity NPC469899
0.5904 Remote Similarity NPC145658
0.5895 Remote Similarity NPC472351
0.5882 Remote Similarity NPC196359
0.5882 Remote Similarity NPC221764
0.5882 Remote Similarity NPC78312
0.5882 Remote Similarity NPC118524
0.5882 Remote Similarity NPC135539
0.5877 Remote Similarity NPC329216
0.5872 Remote Similarity NPC171734
0.5862 Remote Similarity NPC470652
0.5862 Remote Similarity NPC477642
0.5851 Remote Similarity NPC6902
0.5844 Remote Similarity NPC8488
0.5844 Remote Similarity NPC274499
0.5844 Remote Similarity NPC333075
0.5833 Remote Similarity NPC128559
0.5833 Remote Similarity NPC174304
0.5833 Remote Similarity NPC325597
0.5823 Remote Similarity NPC38463
0.5814 Remote Similarity NPC319046
0.5814 Remote Similarity NPC306696
0.5812 Remote Similarity NPC160688
0.5812 Remote Similarity NPC315188
0.5802 Remote Similarity NPC320598
0.5802 Remote Similarity NPC34838
0.5802 Remote Similarity NPC292299
0.5798 Remote Similarity NPC470654
0.5798 Remote Similarity NPC470650
0.5798 Remote Similarity NPC470653
0.5795 Remote Similarity NPC328457
0.5789 Remote Similarity NPC327239
0.5783 Remote Similarity NPC105297
0.5773 Remote Similarity NPC469363
0.5761 Remote Similarity NPC316242
0.5761 Remote Similarity NPC325902
0.5755 Remote Similarity NPC188785
0.5747 Remote Similarity NPC126779
0.5745 Remote Similarity NPC23984
0.5732 Remote Similarity NPC263207
0.573 Remote Similarity NPC55274
0.573 Remote Similarity NPC477643
0.573 Remote Similarity NPC477641
0.573 Remote Similarity NPC320865
0.5727 Remote Similarity NPC296143
0.5727 Remote Similarity NPC207820
0.5714 Remote Similarity NPC289691
0.5699 Remote Similarity NPC478017
0.5699 Remote Similarity NPC315131
0.5699 Remote Similarity NPC315535
0.5684 Remote Similarity NPC246005
0.5684 Remote Similarity NPC284456
0.5679 Remote Similarity NPC11433
0.5679 Remote Similarity NPC245346
0.5679 Remote Similarity NPC302003
0.5663 Remote Similarity NPC477644
0.5657 Remote Similarity NPC473495
0.5657 Remote Similarity NPC52533
0.5644 Remote Similarity NPC476019
0.5641 Remote Similarity NPC190184
0.5641 Remote Similarity NPC197087
0.5641 Remote Similarity NPC477237
0.5625 Remote Similarity NPC235078
0.5625 Remote Similarity NPC251122
0.561 Remote Similarity NPC254541
0.561 Remote Similarity NPC473599
0.56 Remote Similarity NPC155230

  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 NPC475542 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
0.7952 Intermediate Similarity NPD1125 Discovery
0.7634 Intermediate Similarity NPD8038 Phase 2
0.7614 Intermediate Similarity NPD3177 Phase 3
0.7586 Intermediate Similarity NPD7759 Phase 2
0.7586 Intermediate Similarity NPD7760 Phase 2
0.7556 Intermediate Similarity NPD4261 Phase 1
0.7356 Intermediate Similarity NPD9577 Approved
0.7215 Intermediate Similarity NPD322 Phase 1
0.7011 Intermediate Similarity NPD7763 Phase 2
0.7011 Intermediate Similarity NPD7762 Phase 2
0.6989 Remote Similarity NPD4780 Clinical (unspecified phase)
0.6932 Remote Similarity NPD2683 Discontinued
0.69 Remote Similarity NPD6122 Discontinued
0.6875 Remote Similarity NPD7841 Clinical (unspecified phase)
0.6829 Remote Similarity NPD2220 Clinical (unspecified phase)
0.6813 Remote Similarity NPD3723 Clinical (unspecified phase)
0.6667 Remote Similarity NPD1456 Approved
0.6456 Remote Similarity NPD574 Approved
0.641 Remote Similarity NPD8951 Approved
0.6375 Remote Similarity NPD575 Clinical (unspecified phase)
0.6364 Remote Similarity NPD9425 Approved
0.631 Remote Similarity NPD620 Approved
0.6265 Remote Similarity NPD1429 Clinical (unspecified phase)
0.6235 Remote Similarity NPD9649 Approved
0.6076 Remote Similarity NPD9433 Approved
0.6064 Remote Similarity NPD3733 Clinical (unspecified phase)
0.6053 Remote Similarity NPD9205 Approved
0.6053 Remote Similarity NPD9204 Approved
0.6044 Remote Similarity NPD4815 Discontinued
0.5921 Remote Similarity NPD61 Approved
0.5921 Remote Similarity NPD8846 Approved
0.5921 Remote Similarity NPD8847 Approved
0.5882 Remote Similarity NPD8868 Approved
0.5862 Remote Similarity NPD1439 Clinical (unspecified phase)
0.5843 Remote Similarity NPD366 Approved
0.5833 Remote Similarity NPD348 Approved
0.5814 Remote Similarity NPD337 Discontinued
0.5814 Remote Similarity NPD4241 Registered
0.581 Remote Similarity NPD6120 Clinical (unspecified phase)
0.5806 Remote Similarity NPD9578 Clinical (unspecified phase)
0.58 Remote Similarity NPD2682 Approved
0.5789 Remote Similarity NPD882 Phase 2
0.5789 Remote Similarity NPD883 Phase 2
0.5773 Remote Similarity NPD5791 Phase 2
0.5769 Remote Similarity NPD3714 Approved
0.5769 Remote Similarity NPD3713 Approved
0.5769 Remote Similarity NPD3715 Approved
0.5761 Remote Similarity NPD3160 Suspended
0.5747 Remote Similarity NPD4242 Approved
0.5745 Remote Similarity NPD3628 Phase 3
0.573 Remote Similarity NPD2256 Clinical (unspecified phase)
0.573 Remote Similarity NPD6944 Clinical (unspecified phase)
0.5699 Remote Similarity NPD7918 Clinical (unspecified phase)
0.5699 Remote Similarity NPD7917 Clinical (unspecified phase)
0.5698 Remote Similarity NPD886 Clinical (unspecified phase)
0.5679 Remote Similarity NPD8865 Approved
0.5673 Remote Similarity NPD1784 Approved
0.567 Remote Similarity NPD9401 Discovery
0.5663 Remote Similarity NPD3192 Approved
0.5663 Remote Similarity NPD3193 Approved
0.5658 Remote Similarity NPD8950 Approved
0.5644 Remote Similarity NPD5792 Clinical (unspecified phase)
0.5641 Remote Similarity NPD8785 Approved
0.5631 Remote Similarity NPD8394 Approved
0.5618 Remote Similarity NPD9446 Approved
0.5612 Remote Similarity NPD619 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