Citations in PubMed

Primary Citation PubMed: 7708670 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 9

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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Computer-based screening of functional conformers of proteins.

(2008) PLoS Comput Biol 4

PubMed: 18463705 | PubMedCentral: PMC2265533 | DOI: 10.1371/journal.pcbi.1000009

For the HIV protease, 73 experimentally determined crystal structures were used: 1a30, 1a8g, 1a9m, 1aaq, 1ajv, 1ajx, 1axa, 1bdr, 1bv7, 1bv9, 1bwa, 1bwb, 1cpi, 1dif, 1dmp, 1gnm, 1gnn, 1gno, 1hbv, 1hih,... 1hiv, 1hos, 1hps, 1hpv, 1hpx, 1hsg, 1hte, 1htf, 1htg, 1hvc, 1hvi, 1hvj, 1hvk, 1hvl, 1hvr, 1hvs, 1hwr, 1hxb, 1hxw, 1mer, 1mes, 1met, 1meu, 1mtr, 1odw, 1odx, 1ody, 1ohr, 1pro, 1qbr, 1qbs, 1qbt, 1qbu, 1sbg, 1tcx, 1vij, 1vik, 1ytg, 1yth, 2aid, 2bpv, 2bpw, 2bpx, 2bpy, 2bpz, 2upj, 3aid, 4hvp, 4phv, 5hvp, 7hvp, 8hvp, 9hvp.

Publication Year: 2008


A knowledge-guided strategy for improving the accuracy of scoring functions in binding affinity prediction.

(2010) BMC Bioinformatics 11

PubMed: 20398404 | PubMedCentral: PMC2868011 | DOI: 10.1186/1471-2105-11-193

Table 1 PDB codes of the protein-ligand complexes in the three test sets HIV protease complexes ( N = 112) 1GNM , 1GNN , 1GNO , 1A30 , 1A9M , 1AAQ , 1AJV , 1AJX , 1B6J , 1B6K , 1B6L , 1B6M , 1BDQ , 1B... 7 , 1BV9 , 1BWA , 1BWB , 1C70 , 1D4K , 1D4L , 1D4Y , 1DIF , 1DMP , 1G2K , 1G35 , 1HBV , 1HEG , 1HIH , 1HII , 1HOS , 1HPO , 1HPS , 1HPV , 1HPX , 1HSH , 1HVH , 1HVI , 1HVJ , 1HVK , 1HVL , 1HVR , 1HVS , 1HWR , 1HXB , 1HXW , 1IIQ , 1IZH , 1IZI , 1LZQ , 1MES , 1MET , 1MEU , 1MRW , 1MRX , 1MSM , 1MSN , 1MTR , 1NH0 , 1ODY , 1OHR , 1PRO , 1QBR , 1QBS , 1QBT , 1QBU , 1SBG , 1SDT , 1SDU , 1SDV , 1SGU , 1SH9 , 1T7J , 1W5V , 1W5W , 1W5X , 1W5Y , 1Z1H , 1Z1R , 1ZP8 , 1ZPA , 1ZSF , 1ZSR , 2AOC , 2AOD , 2AOE , 2AQU , 2AVM , 2AVO , 2AVQ , 2AVS , 2AVV , 2BPV , 2BPY , 2BQV , 2F80 , 2F81 , 2F8G , 2FGU , 2FGV , 2HB3 , 2I0A , 2I0D , 7HVP , 7UPJ , 2HS2 , 2AOG , 2HS1 , 1A94 , 1AID , 1KZK , 1TCX , 3AID Trypsin complexes ( N = 73) 1C1R , 1C5P , 1C5Q , 1C5S , 1C5T , 1CE5 , 1F0T , 1F0U , 1K1I , 1K1J , 1K1L , 1K1M , 1K1N , 1OSS , 1PPC , 1PPH , 1QB1 , 1QB6 , 1QB9 , 1QBN , 1QBO , 1TNG , 1TNH , 1TNI , 1TNJ , 1TNK , 1TNL , 1V2J , 1V2K , 1V2L , 1V2N , 1V2Q , 1V2R , 1V2S , 1V2T , 1V2U , 1V2W , 2A31 , 2BZA , 2FX6 , 1BRA , 1G3B , 1G3C , 1G3D , 1G3E , 1GHZ , 1GI1 , 1GI4 , 1GI6 , 1GJ6 , 1J16 , 1J17 , 1O2H , 1O2J , 1O2K , 1O2N , 1O2O , 1O2Q , 1O2S , 1O2W , 1O2X , 1O2Z , 1O30 , 1O33 , 1O36 , 1O38 , 1O3D , 1O3F , 1O3H , 1O3I , 1O3J , 1O3K , 1V2O Carbonic anhydrase complexes ( N = 44) 1BN1 , 1BN3 , 1BN4 , 1BNN , 1BNQ , 1BNT , 1BNU , 1BNV , 1BNW , 1A42 , 1AVN , 1BCD , 1CIL , 1CIM , 1CIN , 1CNW , 1CNX , 1CNY , 1G1D , 1G45 , 1G46 , 1G48 , 1G4J , 1G4O , 1G52 , 1G53 , 1G54 , 1I9L , 1I9M , 1I9N , 1I9O , 1I9P , 1I9Q , 1IF7 , 1IF8 , 1OKL , 1TTM , 1XPZ , 1XQ0 , 1YDA , 1YDB , 1YDD , 2EZ7 , 2H4N In addition, a set of putative binding poses were prepared for the ligand molecule in each complex in all three test sets.

Publication Year: 2010


Strength of hydrogen bond network takes crucial roles in the dissociation process of inhibitors from the HIV-1 protease binding pocket.

(2011) PLoS One 6

PubMed: 21559397 | PubMedCentral: PMC3084818 | DOI: 10.1371/journal.pone.0019268

Methods MD simulations The structures for the inhibitor bound complexes were retrieved from Protein Data Bank with PDB codes: 1AJX [32] for AHA001 bound complex, 1HVR [33�... d; for XK263 bound complex and 1HXW [34] for ABT538 bound complex.

Publication Year: 2011


Dynamical basis for drug resistance of HIV-1 protease.

(2011) BMC Struct Biol 11

PubMed: 21740562 | PubMedCentral: PMC3149572 | DOI: 10.1186/1472-6807-11-31

Table 2 Clustering results of the ten bound forms PDB id Mutation RMSD (Å) Coupled with the active site Coupled with the flap region 2FNS 7 (substrate) Q7K, D25N, L63P, I64V 0.52 10 23 24 25 2... 27 28 29 30 31 84 85 86 87 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83 1HPV 6 (Amprenavir) None 0.54 10 23 24 25 26 27 28 29 30 31 32 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83 84 1HXB 6 (Saquinavir) None 0.31 10 23 24 25 26 27 28 29 30 31 32 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83 84 1MUI 5 (Lopinavir) N37S 0.53 10 23 24 25 26 27 28 29 30 31 32 84 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83 2O4K 8 (Atazanavir) Q7K 0.35 23 24 25 26 27 28 29 30 31 32 83 84 85 86 87 88 89 90 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 76 77 78 79 80 81 82 3JVY 6 (Darunavir) Q7K, L33I*, L63I, C67A, G86A, C95A 0.38 23 24 25 26 27 28 29 30 31 32 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 79 80 81 82 83 84 2O4P 8 (Tipranavir) Q7K 0.39 23 24 25 26 27 28 29 30 31 32 83 84 85 86 87 88 89 90 44 45 46 47 48 49 50 51 52 53 54 55 56 79 80 81 82 83 84 1HXW 6 (Ritonavir) None 0.40 10 23 24 25 26 27 28 29 30 31 85 86 87 44 45 46 47 48 49 50 51 52 53 54 55 56 79 80 81 82 83 84 2PYN 6 (Nelfinavir) D30N, A71V* 0.26 10 23 24 25 26 27 28 29 30 31 32 84 85 86 44 45 46 47 48 49 50 51 52 53 54 55 56 78 79 80 81 82 83 2B7Z 7 (Indinavir) K20R*, V32I*, L33F*, M36I*, M46I*, L63P, A71V*,V82A*, I84V*, L90M* 0.32 10 22 23 24 25 26 27 28 29 84 85 86 34 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 76 77 78 79 80 81 82 83 The type of the ligand is listed in brackets.

Publication Year: 2011


Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design.

(2012) PLoS Comput Biol 8

PubMed: 22927804 | PubMedCentral: PMC3426558 | DOI: 10.1371/journal.pcbi.1002639

Generation of backrub structural ensembles Computational ensembles of “near-native" backbones were generated starting from one of 11 crystallographic structures of the HIV-1 protease consensus... sequence (1A8G, 1EBY, 1HXW, 1IZH, 1PRO, 1SBG, 1VIJ, 1VIK, 4PHV, 5HVP and 9HVP) and one of five structures of reverse transcriptase (1HNI, 1HPZ, 1IKX, 2B6A and 2BAN) by using the previously described backrub protocol [20] , [22] .

Publication Year: 2012


Towards ligand docking including explicit interface water molecules.

(2013) PLoS One 8

PubMed: 23840735 | PubMedCentral: PMC3695863 | DOI: 10.1371/journal.pone.0067536

The structure shown was downloaded from the protein databank (PDB ID: 1HXW).

Publication Year: 2013


Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors.

(2014) J Chem Theory Comput 10

PubMed: 24683369 | PubMedCentral: PMC3966525 | DOI: 10.1021/ct4007037

Table 1 The PDB Codes of the Crystal Structures Used to Provide Coordinates for the HIV-1 Protease Bound to Each of the Nine FDA-Approved Protease Inhibitors drug name abbreviation PDB Amprenavir APV ... HPV Atazanavir AZV 2AQU Darunavir DRV 2HSI Indinavir IDV 1HSG Lopinavir LPV 1MUI Nelfinavir NFV 1OHR Ritonavir RTV 1HXW Saquinavir SQV 1FB7 Tipranavir TPV 2O4P Protein parameters were taken from the standard AMBER force field for bioorganic systems (ff03).

Publication Year: 2014


Intradimer/Intermolecular interactions suggest autoinhibition mechanism in endophilin A1.

(2014) J Am Chem Soc 136

PubMed: 24568626 | PubMedCentral: PMC3985530 | DOI: 10.1021/ja411607b

For example, the buried interface area of the HIV-1 protease homodimer (PDB: 1hxw) is 1718.7 Å 2 (via PISA) per subunit and is predicted to contain 22 HBs and 7 SBs.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4366505

( c ) Superposition of 1 with 2 (in green, PDB code 4U7V) bound to HIV-1 PR (PDB code 1HXW (ref.

Publication Year: 2015