Citations in PubMed

Primary Citation PubMed: 14664558 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 2

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors.

(2014) J Chem Inf Model 54

PubMed: 24521147 | PubMedCentral: PMC3966529 | DOI: 10.1021/ci4005332

Table 1 K i and K d Binding Affinity Data Set of Protein–Protein Interaction Inhibitors a   interaction biological role PDB (complex) K d (complex) (M)   Bcl-x L /Bak programme... cell death 1bxl 3.4 × 10 –7   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 1 N3B 4369509 Bcl-x L 1ysi 1.2 × 10 –7 2 ABT-737 11228183 Bcl-x L 2yxj 5.0 × 10 –10 3 4FC 2782689 Bcl-x L 1ysg 3.0 × 10 –5 4 TN1 68258 Bcl-x L 1ysg 4.3 × 10 –3 5 LIU 15991562 Bcl-2 2o22 6.7 × 10 –8 6 W1191542 44182311 Bcl-x L 3inq 1.1 × 10 –8   interaction biological role PDB (complex) K d (complex) (M)   MDM2/p53 transcription regulation 1ycr 6.0 × 10 –7   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 7 HDM2 656933 MDM2 1t4e 8.0 × 10 –8 8 WK23 44825260 MDM2 3lbk 9.2 × 10 –7 9 MI-63 72200152 MDM2 3lbl 3.6 × 10 –8   interaction biological role PDB (complex) K d (complex) (M)   XIAP-BIR3/CASPASE-9 programmed cell death 1nw9 2.0 × 10 –8   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 10 998 4369343 XIAP-BIR3 1tfq 1.2 × 10 –8 11 997 5388929 XIAP-BIR3 1tft 5.0 × 10 –9 12 9JZ 72199974 XIAP-BIR3 3hl5 3.4 × 10 –5   interaction biological role PDB (complex) K d (complex) (M)   XIAP-BIR3/SMAC programmed cell death 1g73 4.2 × 10 –7   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥K d (modulator) (M) 13 BI6 72199334 XIAP-BIR3 2jk7 6.7 × 10 –8 14 AoxSPW 24916924 XIAP-BIR3 2opy 3.0 × 10 –5 15 Smac005 25011737 XIAP-BIR3 3clx 1.2 × 10 –7 16 Smac005 25011737 XIAP-BIR3 3cm7 1.2 × 10 –7 17 Smac010 25011738 XIAP-BIR3 3cm2 4.2 × 10 –7 18 Smac037 25058143 XIAP-BIR3 3eyl 2.2 × 10 –7 19 CZ3 72199333 XIAP-BIR3 3g76 2.3 × 10 –7   interaction biological role PDB (complex) K d (complex) (M)   ZipA/FtsZ cell cycle regulation/cellular structure 1f47 2.0 × 10 –5   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 20 WAI 656967 ZipA 1y2f 1.2 × 10 –5 21 CL3 5287936 ZipA 1y2g 8.3 × 10 –5   interaction biological role PDB (complex) K d (complex) (M)   HPV-E2/E1 viral infection 1tue n/d   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 22 BILH 434 5287508 HPV-E2 1r6n 4.0 × 10 –8   interaction biological role PDB (complex) K d (complex) (M)   IL-2/IL-2R immune system regulation 1z92 1.0 × 10 –8   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 23 FRG 5288250 IL-2 1m48 2.2 × 10 –5 24 FRB 23586028 IL-2 1pw6 7.0 × 10 –6 25 SP-1985 5287951 IL-2 1m49 7.5 × 10 –6 26 FRH 5288251 IL-2 1py2 1.0 × 10 –7 27 SP-4160 656989 IL-2 1qvn 1.4 × 10 –6 a Original references for the affinity data are provided in the Supporting Information (Table S1).

Publication Year: 2014


Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.

(2014) PLoS Comput Biol 10

PubMed: 25079060 | PubMedCentral: PMC4117425 | DOI: 10.1371/journal.pcbi.1003741

Interestingly, one IL-2Rα structure (PDB ID: 1pw6) has a Dscore+ that places the target in the low end of the druggable score range, but the pocket volume does not satisfy the drug-like criter... a, and this remains the case after protein flexibility modeling.

Target name PDB ID Ligand type Assigned druggability Crystal pocket Flexible model Dscore+ Volume Dscore+ Volume Bcl-xL 2bzw protein druggable 1.5 112 2.4 172 Bcl-2 2xa0 protein druggable 1.5 167 2.0 174 HDM2 1ycr protein druggable 1.7 165 2.5 175 TNFα 1tnf protein difficult 1.8 126 2.4 257 IL-2Rα 1z92 protein difficult 0.9 49 * * HPV E2 1tue protein difficult 0.8 57 * * ZipA 1f46 protein difficult 0.7 105 * * ZipA 1f47 protein difficult 0.9 141 * * Bcl-xL 2yxj cmpd druggable 1.8 141 2.5 239 Bcl-xL 3qkd cmpd druggable 1.9 132 2.1 195 Bcl-xL 4ehr cmpd druggable 1.4 100 2.4 175 Bcl-2 4aq3 cmpd druggable 1.7 113 2.3 220 HDM2 1rv1 cmpd druggable 1.7 147 2.2 178 HDM2 1t4e cmpd druggable 1.6 203 2.1 234 HDM2 3jzk cmpd druggable 1.6 204 1.9 184 HDM2 3lbk cmpd druggable 1.5 150 1.9 160 HDM2 3lbl cmpd druggable 2.0 224 2.2 218 HDM2 3tu1 cmpd druggable 1.5 221 1.9 172 HDM2 4dij cmpd druggable 1.6 192 1.8 207 HDM2 4ere cmpd druggable 1.8 165 2.5 172 TNFα 2az5 cmpd difficult 1.7 325 2.0 233 TNFR1 1ft4 cmpd difficult 1.2 330 * * IL-2Rα 1py2 cmpd difficult 1.2 66 * * IL-2Rα 1pw6 cmpd difficult 1.4 73 1.4 72 HPV E2 1r6n cmpd difficult 1.2 95 * * ZipA 1y2f cmpd difficult 0.9 91 * * ZipA 1y2g cmpd difficult 0.9 96 * * These targets have protein-protein co-crystal structures shown in the top half of the table, and corresponding protein-ligand co-crystal structures are shown in the bottom half.

Publication Year: 2014