Structure

Physi-Chem Properties

Molecular Weight:  254.04
Volume:  218.528
LogP:  -3.79
LogD:  -0.402
LogS:  -2.593
# Rotatable Bonds:  8
TPSA:  126.64
# H-Bond Aceptor:  6
# H-Bond Donor:  6
# Rings:  0
# Heavy Atoms:  8

MedChem Properties

QED Drug-Likeness Score:  0.328
Synthetic Accessibility Score:  3.629
Fsp3:  0.714
Lipinski Rule-of-5:  Accepted
Pfizer Rule:  Accepted
GSK Rule:  Accepted
BMS Rule:  1
Golden Triangle Rule:  Accepted
Chelating Alert:  0
PAINS Alert:  0

ADMET Properties (ADMETlab2.0)

ADMET: Absorption

Caco-2 Permeability:  -6.558
MDCK Permeability:  2.71419753516966e-06
Pgp-inhibitor:  0.0
Pgp-substrate:  0.461
Human Intestinal Absorption (HIA):  0.015
20% Bioavailability (F20%):  0.001
30% Bioavailability (F30%):  0.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):  0.183
Plasma Protein Binding (PPB):  16.027732849121094%
Volume Distribution (VD):  0.412
Pgp-substrate:  80.43682861328125%

ADMET: Metabolism

CYP1A2-inhibitor:  0.005
CYP1A2-substrate:  0.017
CYP2C19-inhibitor:  0.033
CYP2C19-substrate:  0.042
CYP2C9-inhibitor:  0.102
CYP2C9-substrate:  0.163
CYP2D6-inhibitor:  0.018
CYP2D6-substrate:  0.157
CYP3A4-inhibitor:  0.023
CYP3A4-substrate:  0.01

ADMET: Excretion

Clearance (CL):  7.201
Half-life (T1/2):  0.849

ADMET: Toxicity

hERG Blockers:  0.029
Human Hepatotoxicity (H-HT):  0.03
Drug-inuced Liver Injury (DILI):  0.012
AMES Toxicity:  0.01
Rat Oral Acute Toxicity:  0.068
Maximum Recommended Daily Dose:  0.003
Skin Sensitization:  0.221
Carcinogencity:  0.339
Eye Corrosion:  0.003
Eye Irritation:  0.081
Respiratory Toxicity:  0.098

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General Info & Identifiers & Properties  
Structure MOL file  
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Biological Activities  
Similar NPs/Drugs  

  Natural Product: NPC114990

Natural Product ID:  NPC114990
Common Name*:   (2R)-2-Amino-3-[[(2R)-2-Amino-2-Carboxyethyl]Sulfanylmethylsulfanyl]Propanoic Acid
IUPAC Name:   (2R)-2-amino-3-[[(2R)-2-amino-2-carboxyethyl]sulfanylmethylsulfanyl]propanoic acid
Synonyms:  
Standard InCHIKey:  JMQMNWIBUCGUDO-WHFBIAKZSA-N
Standard InCHI:  InChI=1S/C7H14N2O4S2/c8-4(6(10)11)1-14-3-15-2-5(9)7(12)13/h4-5H,1-3,8-9H2,(H,10,11)(H,12,13)/t4-,5-/m0/s1
SMILES:  C([C@@H](C(=O)O)N)SCSC[C@@H](C(=O)O)N
Synthetic Gene Cluster:   n.a.
ChEMBL Identifier:   CHEMBL3138615
PubChem CID:   68134
25203309
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:0000060] Alpha amino acids and derivatives
              • [CHEMONTID:0004313] Cysteine and derivatives
                • [CHEMONTID:0004555] L-cysteine-S-conjugates

*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
NPO5867 Albizzia lophantha n.a. n.a. n.a. n.a. n.a. n.a. Database[HerDing]
NPO5867 Albizzia lophantha n.a. n.a. n.a. n.a. n.a. n.a. Database[TCMID]
NPO5867 Albizzia lophantha n.a. n.a. n.a. n.a. n.a. n.a. Database[TCM_Taiwan]

☑ 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
NPT368 Cell Line SN12C Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT370 Cell Line NCI-H23 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT371 Cell Line UO-31 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT116 Cell Line HL-60 Homo sapiens GI50 n.a. 184501.54 nM PMID[463867]
NPT372 Cell Line HOP-92 Homo sapiens GI50 n.a. 168655.3 nM PMID[463867]
NPT374 Cell Line SF-539 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT373 Cell Line SK-MEL-5 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT375 Cell Line Malme-3M Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT111 Cell Line K562 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT376 Cell Line A498 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT112 Cell Line MOLT-4 Homo sapiens GI50 n.a. 195433.95 nM PMID[463867]
NPT377 Cell Line OVCAR-3 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT379 Cell Line HOP-62 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT378 Cell Line NCI/ADR-RES Homo sapiens GI50 n.a. 104472.02 nM PMID[463867]
NPT381 Cell Line OVCAR-8 Homo sapiens GI50 n.a. 35645.11 nM PMID[463867]
NPT380 Cell Line U-251 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT382 Cell Line OVCAR-5 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT383 Cell Line SNB-19 Homo sapiens GI50 n.a. 174180.69 nM PMID[463867]
NPT572 Cell Line DMS-273 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT573 Cell Line M19-MEL Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT323 Cell Line SW-620 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT455 Cell Line NCI-H522 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT386 Cell Line KM12 Homo sapiens GI50 n.a. 126473.63 nM PMID[463867]
NPT574 Cell Line XF498 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT388 Cell Line NCI-H322M Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT389 Cell Line RPMI-8226 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT456 Cell Line OVCAR-4 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT390 Cell Line LOX IMVI Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT168 Cell Line P388 Mus musculus GI50 n.a. 71121.35 nM PMID[463867]
NPT575 Cell Line KM-20L2 Homo sapiens GI50 n.a. 163681.65 nM PMID[463867]
NPT147 Cell Line SK-MEL-2 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT391 Cell Line HCC 2998 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT81 Cell Line A549 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT392 Cell Line SNB-75 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT393 Cell Line HCT-116 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT148 Cell Line HCT-15 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT394 Cell Line EKVX Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT395 Cell Line SF-268 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT83 Cell Line MCF7 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT576 Cell Line DMS-114 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT146 Cell Line SK-OV-3 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT397 Cell Line NCI-H460 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT398 Cell Line UACC-62 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT552 Cell Line P388/ADR Mus musculus GI50 n.a. 224905.46 nM PMID[463867]
NPT308 Cell Line CAKI-1 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT399 Cell Line SF-295 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT458 Cell Line IGROV-1 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT578 Cell Line SNB-78 Homo sapiens GI50 n.a. 126473.63 nM PMID[463867]
NPT403 Cell Line UACC-257 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT404 Cell Line CCRF-CEM Homo sapiens GI50 n.a. 89536.48 nM PMID[463867]
NPT579 Cell Line DLD-1 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT139 Cell Line HT-29 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT405 Cell Line NCI-H226 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT170 Cell Line SK-MEL-28 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT407 Cell Line COLO 205 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT406 Cell Line RXF 393 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT732 Cell Line HOP-18 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT738 Cell Line SN12K1 Homo sapiens GI50 n.a. 224905.46 nM PMID[463867]
NPT73 Individual Protein Solute carrier organic anion transporter family member 1B1 Homo sapiens Inhibition = 92.41 % PMID[463868]
NPT72 Individual Protein Solute carrier organic anion transporter family member 1B3 Homo sapiens Inhibition = 96.92 % PMID[463868]

☑ 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 NPC114990 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
0.913 High Similarity NPC185755
0.913 High Similarity NPC213876
0.8936 High Similarity NPC204364
0.8571 High Similarity NPC152451
0.8571 High Similarity NPC193989
0.8571 High Similarity NPC170739
0.84 Intermediate Similarity NPC125736
0.8113 Intermediate Similarity NPC102815
0.8077 Intermediate Similarity NPC317815
0.7959 Intermediate Similarity NPC49952
0.7959 Intermediate Similarity NPC198196
0.7959 Intermediate Similarity NPC228932
0.7959 Intermediate Similarity NPC136476
0.7925 Intermediate Similarity NPC145235
0.7872 Intermediate Similarity NPC326808
0.7872 Intermediate Similarity NPC254482
0.7872 Intermediate Similarity NPC317691
0.7872 Intermediate Similarity NPC110533
0.7719 Intermediate Similarity NPC321419
0.75 Intermediate Similarity NPC82239
0.75 Intermediate Similarity NPC283786
0.7451 Intermediate Similarity NPC118187
0.7358 Intermediate Similarity NPC319175
0.7308 Intermediate Similarity NPC318523
0.7059 Intermediate Similarity NPC191136
0.6939 Remote Similarity NPC326992
0.6939 Remote Similarity NPC121517
0.6939 Remote Similarity NPC168375
0.6939 Remote Similarity NPC53449
0.6939 Remote Similarity NPC237525
0.6939 Remote Similarity NPC326212
0.6809 Remote Similarity NPC116709
0.6809 Remote Similarity NPC272614
0.6809 Remote Similarity NPC21290
0.6731 Remote Similarity NPC329263
0.6667 Remote Similarity NPC167986
0.6667 Remote Similarity NPC291186
0.6667 Remote Similarity NPC63621
0.6604 Remote Similarity NPC297220
0.6604 Remote Similarity NPC248970
0.6604 Remote Similarity NPC306238
0.6538 Remote Similarity NPC198301
0.6538 Remote Similarity NPC132307
0.6538 Remote Similarity NPC126925
0.6538 Remote Similarity NPC325097
0.6508 Remote Similarity NPC289691
0.6481 Remote Similarity NPC136159
0.6481 Remote Similarity NPC181588
0.6415 Remote Similarity NPC285322
0.6415 Remote Similarity NPC118459
0.6415 Remote Similarity NPC327698
0.6415 Remote Similarity NPC208793
0.6406 Remote Similarity NPC325597
0.6406 Remote Similarity NPC174304
0.6364 Remote Similarity NPC153370
0.6364 Remote Similarity NPC140872
0.6364 Remote Similarity NPC93081
0.6275 Remote Similarity NPC66043
0.6269 Remote Similarity NPC126779
0.625 Remote Similarity NPC112890
0.625 Remote Similarity NPC316231
0.625 Remote Similarity NPC324825
0.6207 Remote Similarity NPC329495
0.6182 Remote Similarity NPC316168
0.617 Remote Similarity NPC14778
0.6154 Remote Similarity NPC226265
0.6154 Remote Similarity NPC219143
0.614 Remote Similarity NPC273330
0.614 Remote Similarity NPC137958
0.614 Remote Similarity NPC315977
0.6122 Remote Similarity NPC9294
0.6119 Remote Similarity NPC319046
0.6087 Remote Similarity NPC16947
0.6 Remote Similarity NPC327831
0.6 Remote Similarity NPC309658
0.5965 Remote Similarity NPC174246
0.5965 Remote Similarity NPC270805
0.5965 Remote Similarity NPC162620
0.5965 Remote Similarity NPC328378
0.5965 Remote Similarity NPC226027
0.5965 Remote Similarity NPC286989
0.5965 Remote Similarity NPC245027
0.5965 Remote Similarity NPC93888
0.5965 Remote Similarity NPC84636
0.5965 Remote Similarity NPC62045
0.5965 Remote Similarity NPC43204
0.5932 Remote Similarity NPC190184
0.5932 Remote Similarity NPC197087
0.5902 Remote Similarity NPC325985
0.5882 Remote Similarity NPC18188
0.5833 Remote Similarity NPC183845
0.5833 Remote Similarity NPC60672
0.5833 Remote Similarity NPC316889
0.5833 Remote Similarity NPC322091
0.5833 Remote Similarity NPC114517
0.5833 Remote Similarity NPC321118
0.5833 Remote Similarity NPC279661
0.5775 Remote Similarity NPC315897
0.5741 Remote Similarity NPC107645
0.5738 Remote Similarity NPC2801
0.5738 Remote Similarity NPC10915
0.5686 Remote Similarity NPC69179
0.5652 Remote Similarity NPC126681
0.5645 Remote Similarity NPC38463
0.5625 Remote Similarity NPC321536

  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 NPC114990 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
0.9149 High Similarity NPD8873 Approved
0.913 High Similarity NPD8982 Approved
0.8571 High Similarity NPD8802 Approved
0.8571 High Similarity NPD8803 Clinical (unspecified phase)
0.8571 High Similarity NPD9021 Approved
0.84 Intermediate Similarity NPD9025 Approved
0.8077 Intermediate Similarity NPD8849 Clinical (unspecified phase)
0.7959 Intermediate Similarity NPD9020 Approved
0.7872 Intermediate Similarity NPD8215 Approved
0.7872 Intermediate Similarity NPD8214 Approved
0.7368 Intermediate Similarity NPD8848 Approved
0.7037 Intermediate Similarity NPD329 Discontinued
0.6981 Remote Similarity NPD8577 Discontinued
0.6923 Remote Similarity NPD8801 Approved
0.6809 Remote Similarity NPD8210 Phase 3
0.6809 Remote Similarity NPD8211 Approved
0.6786 Remote Similarity NPD9386 Approved
0.6667 Remote Similarity NPD8804 Approved
0.6667 Remote Similarity NPD9213 Approved
0.6667 Remote Similarity NPD8805 Approved
0.6667 Remote Similarity NPD9214 Phase 3
0.6615 Remote Similarity NPD9452 Clinical (unspecified phase)
0.6604 Remote Similarity NPD8870 Approved
0.6567 Remote Similarity NPD2262 Clinical (unspecified phase)
0.6538 Remote Similarity NPD8798 Approved
0.6481 Remote Similarity NPD8810 Clinical (unspecified phase)
0.6415 Remote Similarity NPD8610 Approved
0.6406 Remote Similarity NPD348 Approved
0.6364 Remote Similarity NPD8614 Approved
0.6364 Remote Similarity NPD8808 Approved
0.6364 Remote Similarity NPD8809 Approved
0.6364 Remote Similarity NPD4241 Registered
0.629 Remote Similarity NPD902 Approved
0.6269 Remote Similarity NPD4242 Approved
0.625 Remote Similarity NPD9044 Approved
0.6212 Remote Similarity NPD886 Clinical (unspecified phase)
0.6207 Remote Similarity NPD9420 Clinical (unspecified phase)
0.6182 Remote Similarity NPD8208 Clinical (unspecified phase)
0.6182 Remote Similarity NPD8209 Phase 2
0.6154 Remote Similarity NPD8216 Approved
0.6154 Remote Similarity NPD8217 Clinical (unspecified phase)
0.614 Remote Similarity NPD8871 Approved
0.614 Remote Similarity NPD8872 Phase 3
0.6119 Remote Similarity NPD337 Discontinued
0.5965 Remote Similarity NPD9017 Approved
0.5965 Remote Similarity NPD8624 Approved
0.5965 Remote Similarity NPD9018 Approved
0.5965 Remote Similarity NPD9016 Clinical (unspecified phase)
0.5932 Remote Similarity NPD8785 Approved
0.5932 Remote Similarity NPD8851 Phase 1
0.5926 Remote Similarity NPD8869 Approved
0.5882 Remote Similarity NPD8623 Phase 1
0.5849 Remote Similarity NPD8609 Approved
0.5797 Remote Similarity NPD1815 Discontinued
0.5775 Remote Similarity NPD1825 Clinical (unspecified phase)
0.5714 Remote Similarity NPD9433 Approved
0.5652 Remote Similarity NPD7371 Approved
0.5641 Remote Similarity NPD7643 Phase 1

  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