Structure

Physi-Chem Properties

Molecular Weight:  800.45
Volume:  763.853
LogP:  -5.221
LogD:  -1.247
LogS:  -1.746
# Rotatable Bonds:  26
TPSA:  397.64
# H-Bond Aceptor:  23
# H-Bond Donor:  19
# Rings:  3
# Heavy Atoms:  23

MedChem Properties

QED Drug-Likeness Score:  0.031
Synthetic Accessibility Score:  6.156
Fsp3:  0.758
Lipinski Rule-of-5:  Rejected
Pfizer Rule:  Accepted
GSK Rule:  Rejected
BMS Rule:  2
Golden Triangle Rule:  Rejected
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -5.96
MDCK Permeability:  0.0002843099646270275
Pgp-inhibitor:  0.001
Pgp-substrate:  1.0
Human Intestinal Absorption (HIA):  0.995
20% Bioavailability (F20%):  1.0
30% Bioavailability (F30%):  1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.821
Plasma Protein Binding (PPB):  19.71208953857422%
Volume Distribution (VD):  0.485
Pgp-substrate:  60.61022186279297%

ADMET: Metabolism

CYP1A2-inhibitor:  0.0
CYP1A2-substrate:  0.002
CYP2C19-inhibitor:  0.004
CYP2C19-substrate:  0.023
CYP2C9-inhibitor:  0.0
CYP2C9-substrate:  0.001
CYP2D6-inhibitor:  0.0
CYP2D6-substrate:  0.157
CYP3A4-inhibitor:  0.0
CYP3A4-substrate:  0.003

ADMET: Excretion

Clearance (CL):  1.043
Half-life (T1/2):  0.706

ADMET: Toxicity

hERG Blockers:  0.135
Human Hepatotoxicity (H-HT):  1.0
Drug-inuced Liver Injury (DILI):  0.044
AMES Toxicity:  0.754
Rat Oral Acute Toxicity:  0.015
Maximum Recommended Daily Dose:  0.99
Skin Sensitization:  0.732
Carcinogencity:  0.39
Eye Corrosion:  0.003
Eye Irritation:  0.036
Respiratory Toxicity:  0.746

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

  Natural Product: NPC10897

Natural Product ID:  NPC10897
Common Name*:   (2S,3S,4R)-10-De-O-Carbamoyl-12-O-Carbamoyl-Nbeta-Acetyl Streptothricin D
IUPAC Name:   [(2R,3R,4S,5R,6R)-6-[[(3aS,7R,7aS)-7-hydroxy-4-oxo-1,3a,5,6,7,7a-hexahydroimidazo[4,5-c]pyridin-2-yl]amino]-5-[[(3S)-3-acetamido-6-[[(3S)-3-amino-6-[[(3S)-3,6-diaminohexanoyl]amino]hexanoyl]amino]hexanoyl]amino]-3,4-dihydroxyoxan-2-yl]methyl carbamate
Synonyms:  
Standard InCHIKey:  NCCCZGXVMRHANP-YFZUDYRPSA-N
Standard InCHI:  InChI=1S/C33H60N12O11/c1-16(46)41-19(7-4-10-39-23(49)12-18(36)6-3-9-38-22(48)11-17(35)5-2-8-34)13-24(50)42-27-29(52)28(51)21(15-55-32(37)54)56-31(27)45-33-43-25-20(47)14-40-30(53)26(25)44-33/h17-21,25-29,31,47,51-52H,2-15,34-36H2,1H3,(H2,37,54)(H,38,48)(H,39,49)(H,40,53)(H,41,46)(H,42,50)(H2,43,44,45)/t17-,18-,19-,20+,21+,25+,26-,27+,28-,29-,31+/m0/s1
SMILES:  NCCC[C@@H](CC(=NCCC[C@@H](CC(=NCCC[C@@H](CC(=N[C@H]1[C@H](NC2=N[C@H]3[C@H](N2)C(=NC[C@H]3O)O)O[C@@H]([C@@H]([C@H]1O)O)COC(=N)O)O)N=C(O)C)O)N)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL2088425
PubChem CID:   70693301
Chemical Classification**:  
  • CHEMONTID:0000000 [Organic compounds]
    • [CHEMONTID:0004603] Organic oxygen compounds
      • [CHEMONTID:0000323] Organooxygen compounds
        • [CHEMONTID:0000011] Carbohydrates and carbohydrate conjugates
          • [CHEMONTID:0002105] Glycosyl compounds
            • [CHEMONTID:0002203] Glycosylamines

*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
NPO31206 Streptomyces sp. i08a 1776 Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[21510638]
NPO31206 Streptomyces sp. i08a 1776 Species Streptomycetaceae Bacteria n.a. n.a. n.a. PMID[22939698]

☑ 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
NPT16 Organism Staphylococcus aureus Staphylococcus aureus MIC > 256.0 ug.mL-1 PMID[572122]
NPT175 Organism Enterococcus faecalis Enterococcus faecalis MIC > 256.0 ug.mL-1 PMID[572122]
NPT79 Organism Bacillus subtilis Bacillus subtilis MIC = 64.0 ug.mL-1 PMID[572122]
NPT790 Organism Mycobacterium tuberculosis H37Rv Mycobacterium tuberculosis H37Rv MIC > 256.0 ug.mL-1 PMID[572122]
NPT1107 Organism Mycobacterium smegmatis str. MC2 155 Mycobacterium smegmatis str. MC2 155 MIC > 256.0 ug.mL-1 PMID[572122]
NPT18 Organism Pseudomonas aeruginosa Pseudomonas aeruginosa MIC > 256.0 ug.mL-1 PMID[572122]
NPT3495 Organism Morganella morganii Morganella morganii MIC > 256.0 ug.mL-1 PMID[572122]
NPT19 Organism Escherichia coli Escherichia coli MIC = 64.0 ug.mL-1 PMID[572122]
NPT20 Organism Candida albicans Candida albicans MIC > 256.0 ug.mL-1 PMID[572122]

☑ 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 NPC10897 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 NPC325900
0.9897 High Similarity NPC92874
0.9897 High Similarity NPC62845
0.9897 High Similarity NPC322449
0.9897 High Similarity NPC166242
0.9897 High Similarity NPC189854
0.9794 High Similarity NPC314398
0.9794 High Similarity NPC239705
0.9794 High Similarity NPC314413
0.8624 High Similarity NPC470621
0.8624 High Similarity NPC222481
0.8532 High Similarity NPC259586
0.6923 Remote Similarity NPC57436
0.6923 Remote Similarity NPC121479
0.6777 Remote Similarity NPC313813
0.6636 Remote Similarity NPC216278
0.6387 Remote Similarity NPC59589
0.6372 Remote Similarity NPC330590
0.6328 Remote Similarity NPC94319
0.625 Remote Similarity NPC316807
0.6239 Remote Similarity NPC306838
0.6238 Remote Similarity NPC315806
0.6154 Remote Similarity NPC314772
0.6154 Remote Similarity NPC314968
0.6154 Remote Similarity NPC315036
0.6107 Remote Similarity NPC477518
0.6038 Remote Similarity NPC70574
0.6038 Remote Similarity NPC318258
0.6038 Remote Similarity NPC100204
0.6038 Remote Similarity NPC83248
0.6036 Remote Similarity NPC214376
0.6019 Remote Similarity NPC165119
0.6017 Remote Similarity NPC56298
0.6017 Remote Similarity NPC471628
0.5965 Remote Similarity NPC328646
0.5946 Remote Similarity NPC313552
0.5943 Remote Similarity NPC98750
0.5941 Remote Similarity NPC327486
0.5941 Remote Similarity NPC223174
0.5941 Remote Similarity NPC327753
0.5929 Remote Similarity NPC195969
0.5929 Remote Similarity NPC176381
0.5926 Remote Similarity NPC36927
0.5926 Remote Similarity NPC271772
0.5926 Remote Similarity NPC242077
0.5909 Remote Similarity NPC325750
0.5905 Remote Similarity NPC329077
0.5893 Remote Similarity NPC328806
0.5893 Remote Similarity NPC314408
0.5893 Remote Similarity NPC314007
0.5893 Remote Similarity NPC43850
0.5893 Remote Similarity NPC123746
0.5893 Remote Similarity NPC477060
0.587 Remote Similarity NPC318142
0.5865 Remote Similarity NPC474467
0.5841 Remote Similarity NPC470284
0.5804 Remote Similarity NPC62927
0.5804 Remote Similarity NPC190334
0.5798 Remote Similarity NPC328914
0.5776 Remote Similarity NPC315334
0.5752 Remote Similarity NPC317377
0.5752 Remote Similarity NPC319334
0.5752 Remote Similarity NPC321485
0.5752 Remote Similarity NPC322372
0.5752 Remote Similarity NPC327517
0.5752 Remote Similarity NPC470282
0.5727 Remote Similarity NPC263058
0.5714 Remote Similarity NPC471262
0.5714 Remote Similarity NPC469363
0.5714 Remote Similarity NPC139857
0.5704 Remote Similarity NPC315058
0.5702 Remote Similarity NPC275715
0.5701 Remote Similarity NPC325902
0.5693 Remote Similarity NPC313962
0.569 Remote Similarity NPC208537
0.569 Remote Similarity NPC270005
0.5688 Remote Similarity NPC471420
0.5678 Remote Similarity NPC90240
0.5646 Remote Similarity NPC477519
0.5644 Remote Similarity NPC129100
0.5644 Remote Similarity NPC322801
0.5644 Remote Similarity NPC291650
0.5639 Remote Similarity NPC245534
0.5636 Remote Similarity NPC315969
0.563 Remote Similarity NPC313821
0.563 Remote Similarity NPC75839
0.563 Remote Similarity NPC68327
0.563 Remote Similarity NPC328779
0.5625 Remote Similarity NPC476523
0.561 Remote Similarity NPC221148
0.5606 Remote Similarity NPC477237

  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 NPC10897 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
0.6991 Remote Similarity NPD8045 Clinical (unspecified phase)
0.6923 Remote Similarity NPD35 Approved
0.6923 Remote Similarity NPD4833 Approved
0.6881 Remote Similarity NPD6424 Approved
0.6838 Remote Similarity NPD284 Phase 1
0.6832 Remote Similarity NPD9429 Discontinued
0.6699 Remote Similarity NPD2691 Clinical (unspecified phase)
0.6636 Remote Similarity NPD6426 Approved
0.6636 Remote Similarity NPD6425 Approved
0.6636 Remote Similarity NPD6423 Approved
0.6636 Remote Similarity NPD6427 Approved
0.6606 Remote Similarity NPD6431 Approved
0.6606 Remote Similarity NPD6434 Clinical (unspecified phase)
0.6606 Remote Similarity NPD6433 Approved
0.6606 Remote Similarity NPD6432 Approved
0.6581 Remote Similarity NPD5376 Approved
0.6372 Remote Similarity NPD5377 Approved
0.6372 Remote Similarity NPD5378 Approved
0.6372 Remote Similarity NPD5381 Approved
0.6328 Remote Similarity NPD4826 Approved
0.6328 Remote Similarity NPD4828 Approved
0.6328 Remote Similarity NPD4827 Approved
0.6316 Remote Similarity NPD6428 Approved
0.629 Remote Similarity NPD3204 Clinical (unspecified phase)
0.6275 Remote Similarity NPD9407 Approved
0.6238 Remote Similarity NPD9653 Clinical (unspecified phase)
0.6216 Remote Similarity NPD3716 Discontinued
0.6204 Remote Similarity NPD9654 Phase 2
0.6154 Remote Similarity NPD9434 Approved
0.6154 Remote Similarity NPD9435 Approved
0.6121 Remote Similarity NPD4282 Approved
0.6111 Remote Similarity NPD869 Approved
0.6087 Remote Similarity NPD7844 Discontinued
0.6061 Remote Similarity NPD4816 Clinical (unspecified phase)
0.604 Remote Similarity NPD5386 Phase 2
0.6036 Remote Similarity NPD2698 Approved
0.6018 Remote Similarity NPD6943 Clinical (unspecified phase)
0.6017 Remote Similarity NPD4837 Approved
0.6017 Remote Similarity NPD4835 Approved
0.6017 Remote Similarity NPD4836 Approved
0.6017 Remote Similarity NPD4838 Approved
0.6 Remote Similarity NPD3213 Discontinued
0.598 Remote Similarity NPD9405 Approved
0.5968 Remote Similarity NPD1804 Phase 2
0.5968 Remote Similarity NPD1805 Phase 2
0.5954 Remote Similarity NPD6436 Phase 3
0.595 Remote Similarity NPD6946 Approved
0.595 Remote Similarity NPD2700 Approved
0.5941 Remote Similarity NPD9445 Approved
0.5929 Remote Similarity NPD5796 Clinical (unspecified phase)
0.5929 Remote Similarity NPD5798 Approved
0.5929 Remote Similarity NPD5795 Approved
0.5929 Remote Similarity NPD5797 Approved
0.5929 Remote Similarity NPD5794 Approved
0.5926 Remote Similarity NPD9644 Approved
0.5926 Remote Similarity NPD9645 Approved
0.5926 Remote Similarity NPD9646 Approved
0.5917 Remote Similarity NPD1061 Clinical (unspecified phase)
0.5902 Remote Similarity NPD1428 Phase 2
0.5893 Remote Similarity NPD3202 Approved
0.5893 Remote Similarity NPD3201 Approved
0.5893 Remote Similarity NPD3203 Approved
0.5893 Remote Similarity NPD3208 Approved
0.5893 Remote Similarity NPD3209 Approved
0.5893 Remote Similarity NPD3207 Approved
0.5877 Remote Similarity NPD285 Discontinued
0.5877 Remote Similarity NPD9585 Discontinued
0.5804 Remote Similarity NPD3200 Clinical (unspecified phase)
0.5804 Remote Similarity NPD9603 Phase 3
0.5804 Remote Similarity NPD9602 Phase 3
0.5804 Remote Similarity NPD9604 Approved
0.5798 Remote Similarity NPD1455 Phase 3
0.5798 Remote Similarity NPD223 Clinical (unspecified phase)
0.5798 Remote Similarity NPD1454 Phase 3
0.5784 Remote Similarity NPD2702 Phase 1
0.5784 Remote Similarity NPD2704 Phase 3
0.5738 Remote Similarity NPD4743 Phase 2
0.5727 Remote Similarity NPD4829 Discontinued
0.57 Remote Similarity NPD2703 Discontinued
0.5664 Remote Similarity NPD1760 Approved
0.5645 Remote Similarity NPD1385 Discontinued
0.5644 Remote Similarity NPD373 Approved
0.5644 Remote Similarity NPD374 Approved
0.5644 Remote Similarity NPD9030 Approved
0.5644 Remote Similarity NPD9031 Approved
0.5644 Remote Similarity NPD9033 Approved
0.5644 Remote Similarity NPD9032 Approved
0.5635 Remote Similarity NPD6941 Approved
0.563 Remote Similarity NPD591 Approved
0.563 Remote Similarity NPD3190 Approved
0.563 Remote Similarity NPD3189 Approved
0.563 Remote Similarity NPD3191 Approved
0.563 Remote Similarity NPD577 Phase 3
0.5615 Remote Similarity NPD4830 Approved
0.5615 Remote Similarity NPD4832 Approved
0.5615 Remote Similarity NPD4831 Approved
0.561 Remote Similarity NPD1449 Approved
0.561 Remote Similarity NPD1450 Approved

  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