Citations in PubMed

Primary Citation PubMed: 9393862 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 8

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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Structural insights into the binding of vascular endothelial growth factor-B by VEGFR-1(D2): recognition and specificity.

(2010) J Biol Chem 285

PubMed: 20501651 | PubMedCentral: PMC2911289 | DOI: 10.1074/jbc.M110.130658

The initial search models used were native VEGF-B(10–108) (PDB code 2C7W ) ( 30 ) and VEGFR-1 D2 from VEGF-A in complex with VEGFR-1 D2 complex (PDB code 1FLT ) ( 25 ).

Pairwise superposition of these dimeric growth factors ( Fig. 1 C ) in their receptor-bound state results in an r.m.s.d. of 1.5 Å over 218 C α atoms (PDB code 1FLT ( 25 )) and 2.0 Å over 256 C α atoms (PDB code 1RV6 ( 31 )).

Publication Year: 2010


Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models.

(2010) BMC Bioinformatics 11

PubMed: 20718956 | PubMedCentral: PMC2931518 | DOI: 10.1186/1471-2105-11-429

PDBcode Chain Length Rg S 1HCR A 52 6.92 0.504 1TGS I 56 6.25 0.137 1TGX A 60 6.84 0.158 1ISU A 62 6.02 0.203 1BF4 A 63 6.44 0.223 1PCF A 66 8.33 0.160 1B3A A 67 7.27 0.122 1ATZ A 75 7.24 0.214 1DP7 P... 76 7.35 0.237 3HTS B 82 7.02 0.286 3EIP A 84 7.35 0.233 2BOP A 85 7.90 0.122 1LMB 4 92 7.88 0.235 1FLT Y 94 7.55 0.132 1DIF A 99 7.82 0.260 1IIB A 103 7.38 0.228 1CMB A 104 8.35 0.116 256B A 106 8.37 0.245 1EVH A 111 7.78 0.180 1DPT A 117 8.56 0.194 1FLM B 122 8.26 0.118 2BBK L 124 8.05 0.317 1NWP A 128 7.88 0.179 1BBH A 131 9.18 0.161 1AQZ A 142 8.48 0.208 1A3A D 144 8.15 0.230 1M6P A 146 8.70 0.141 2TNF A 148 9.71 0.252 1ELK A 153 8.62 0.369 1NBC A 155 8.53 0.262 1DPS D 156 9.82 0.272 1PHN A 162 10.48 0.204 1C02 A 166 9.60 0.230 1YTB A 180 11.73 0.190 1BEH B 183 8.78 0.204 1ATL A 200 9.30 0.267 1BSM A 201 10.05 0.191 1YAC B 204 9.80 0.248 6GSV B 217 10.11 0.203 1AUO A 218 9.34 0.137 1QL0 A 241 9.59 0.165 1CYD A 242 10.13 0.287 1TPH 1 245 9.87 0.169 1A28 B 249 10.39 0.300 1C90 A 265 10.30 0.142 1AQU A 281 10.73 0.177 1BF6 B 291 10.21 0.294 1FTR A 296 12.14 0.295 4PGA A 330 11.67 0.217 1CZF A 335 11.43 0.241 S is the difference between the curves resulting from the two-body model and CRYSOL in units of "experimental" standard deviations.

Publication Year: 2010


Tying the knot: the cystine signature and molecular-recognition processes of the vascular endothelial growth factor family of angiogenic cytokines.

(2011) FEBS J 278

PubMed: 21917115 | PubMedCentral: PMC3328748 | DOI: 10.1111/j.1742-4658.2011.08350.x

The structures shown are VEGF-A 8–109 •VEGFR-1 D2 complex (1FLT; [ 67 ]), VEGF-B 10–108 •VEGFR-1 D2 complex (2XAC; [ 72 ]), PlGF-1•VEGFR-1 D2 complex (1RV6; [ 7... ]), and VEGF-C•VEGFR-2 D2D3 complex (2X1W; [ 74 ]).

Publication Year: 2011


The extent and importance of intragenic recombination.

(2004) Hum Genomics 1

PubMed: 15606996 | PubMedCentral: PMC3500195 | DOI: null

In the case of vegf , 3D-PSSM identifies two folds, 1FLTv (PDB ID 1FLT , chain v) and 1VGH with 100 per cent and 91 per cent sequence identity, respectively.

Publication Year: 2004


Use of natural molecules as anti-angiogenic inhibitors for vascular endothelial growth factor receptor.

(2012) Bioinformation 8

PubMed: 23275729 | PubMedCentral: PMC3532009 | DOI: 10.6026/97320630081249

Crystal structure of vascular endothelial growth factor receptor (PDB id: 1FLT ( Figure 1b ) was retrieved from protein data bank.

Q site finder : Crystal structure of VEGFR is not co-crystallized, so Q-site finder was used to find out the possible binding pockets in the VEGFR (PDB id: 1FLT).

Citation: Chatterjee & Bhattacharjee, Bioinformation 8(25): 1249-1254 (2012) References 1 http://www.medicinenet.co 2 http://www.nap.edu 3 P Carmeliet Nat Med 2003 9 653 12778163 4 N Rahimi Exp Eye Res 2006 83 1005 16713597 5 AK Olsson Nat Rev Mol Cell Biol 2006 7 359 16633338 6 MJ Lee Cell 1999 99 301 10555146 7 T Tanimoto J Biol Chem 2002 277 42997 12226078 8 M Autiero Nat Med 2003 9 936 12796773 9 ZG Jin Circ Res 2003 93 354 12893742 10 S Soker Cell 1998 92 735 9529250 11 P Carmeliet Cell 1999 98 147 10428027 12 R Soldi EMBO J 1999 18 882 10022831 13 S Weis J Clin Invest 2004 113 885 15067321 14 SM Weis DA Cheresh Nature 2005 437 497 16177780 15 E Tzima Nature 2005 437 426 16163360 16 R Zhang J Biol Chem 2003 278 51267 14532277 17 Y He J Clin Invest 2006 116 2344 16932810 18 B Dome Am J Pathol 2007 170 1 17200177 19 KL Meadows HI Hurwitz Cold Spring Harb Perspect Med 2012 2 a006577 23028128 Figure 1 (a) Bar graph representing Lipinski rule of five for top 9 anti-angiogenic natural compounds screened through HEX; (b) Cartoon representation of VEGF receptor (PDB Id: 1FLT), binding site highlighted in black balls and inset representation of binding site in red; (c) Bar graph representing HEX docking score for top 9 anti-angiogenic natural compounds; (d) Graphical representation of amino acid and hydrogen bond analysis for the anti-angiogenic natural compound (Npf- 86i) using SwissPDBViewer; (e) Binding site analysis for the VEGF receptor using Q-site server prediction; (f) Bar graph representing QUANTUM docking score for top 9 anti-angiogenic natural compounds screened through HEX, (g) ADME property of top 9 antiangiogenic natural compounds screened through HEX; (h) Pie-chart representation for percentage distribution of drug binding to plasma protein – humans, (The Compound Id represented in the bar graphs along with the color code used is same as represented in Table 1 ).

Publication Year: 2012


HopDock: a probabilistic search algorithm for decoy sampling in protein-protein docking.

(2013) Proteome Sci 11

PubMed: 24564839 | PubMedCentral: PMC3909090 | DOI: 10.1186/1477-5956-11-S1-S6

PDB ID (Chains) HopDock (HH:MM) pyDock [ 4 ] (HH:MM) ClusPro [ 6 ] (HH:MM) 1C1Y (A,B) 04:00 01:30 00:53 1DS6 (A,B) 06:26 02:00 01.30 1TX4 (A,B) 10:42 02:30 01:00 1WWW (W,Y) 03:12 01:00 00:53 1FLT (V,Y... 02:36 00:30 00:53 1IKN (A,C) 06:00 01:30 01.24 1IKN (C,D) 03:54 00:18 01.24 1VCB (A,B) 01:04 00:33 00.54 1VCB (B,C) 01:36 01:08 00:58 1OHZ (A,B) 00:57 02:30 01:00 1T6G (A,C) 11:04 04:00 00:59 1ZHI (A,B) 03:17 04:45 00:59 2HQS (A,C) 12:07 01:00 01:00 1QAV (A,B) 01:05 01:30 00:40 1G4Y (B,R) 03:13 05:29 00:59 1CSE (E,I) 02:48 02:00 00:38 1G4U (R,S) 09:19 01:14 01:26 Timing comparison (HH:MM) of HopDock to other web servers is presented on each of the seventeen systems studied here.

[ 16 ] (Å) pyDock [ 4 ] (Å) ClusPro [ 6 ] (Å) HopDock (Å) 1C1Y (A,B) 2034 1.2 1.3 10.4 7.2 1.9 1DS6 (A,B) 2839 1.2 1.8 0.8 1.7 3.4 1TX4 (A,B) 2957 1.4 2.4 18.5 4.7 1.0 1WWW (W,Y) 1644 11.4 2.2 18.2 17.2 2.2 1FLT (V,Y) 1528 1.5 1.1 2.8 4.7 1.5 1IKN (A,C) 3178 1.2 2.0 20.1 19.7 2.2 1IKN (C,D) 2505 2.0 2.0 16.7 20.9 4.6 1VCB (A,B) 1447 0.7 2.1 1.4 1.9 3.6 1VCB (B,C) 1846 1.3 1.3 22.7 1.9 1.7 1OHZ (A,B) 1443 1.8 1.7 7.5 3.3 2.2 1T6G (A,C) 4022 1.6 2.5 0.1 14.8 2.5 1ZHI (A,B) 2633 25.3 1.7 23.8 24.1 3.3 2HQS (A,C) 3983 29.1 2.2 15.2 16.6 2.6 1QAV (A,B) 1503 1.4 1.0 9.6 1.7 2.6 1G4Y (B,R) 1838 0.8 2.3 26.2 1.9 4.1 1CSE (E,I) 2442 0.7 1.5 13.2 1.1 2.7 1G4U (R,S) 4188 1.0 2.2 27.6 16.1 5.6 A comparative analysis has been performed on all seventeen dimers.

Triangles lRMSD (Å) Rrest - Rinterface 1FLT (V,Y) 0.25 2417 2.06 6.67 0.50 2338 1.12 -3.50 0.75 2080 1.03 1.27 1WWW (W, Y) 0.25 2900 2.29 -18.37 0.50 2911 2.24 -7.45 0.75 2854 2.60 6.62 1C1Y (A,B) 0.25 3385 1.89 -13.65 0.50 3325 1.30 -38.64 0.75 3306 1.45 -21.01 Table shows the effect of three different conservation thresholds 0.25, 0.5, and 0.75 on the number of active triangles and lowest lRMSD to native structure.

PDB ID (Chains) Size(Number of Atoms) Functional Classification 1C1Y (A,B) 1376, 658 Signaling Protein 1DS6 (A,B) 1413, 1426 Signaling Protein 1TX4 (A,B) 1579, 1378 Complex(gtpase Activatn/proto Oncogene) 1WWW (W,Y) 862, 782 Nerve Growth Factor/trka Complex 1FLT (V,Y) 770, 758 Complex (growth Factor/transferase) 1IKN (A,C) 2262, 916 Transcription Factor 1IKN (C,D) 916, 1589 Transcription Factor 1VCB (A,B) 755, 692 Transcription 1VCB (B,C) 692, 1154 Transcription 1OHZ * (A,B) 1027, 416 Cell Adhesion 1T6G * (A,C) 2628, 1394 Hydrolase Inhibitor 1ZHI * (A,B) 1597, 1036 Transcription/replication 2HQS * (A,C) 3127, 856 Transport Protein/lipoprotein 1QAV (A,B) 663, 840 Membrane Protein/oxidoreductase 1G4Y (B,R) 682, 1156 Signaling Protein 1CSE (E,I) 1920, 522 Complex(serine Proteinase Inhibitor) 1G4U (R,S) 1398, 2790 Signaling Protein Details are provided on the dimers selected in this study.

Publication Year: 2013


Modulation, bioinformatic screening, and assessment of small molecular peptides targeting the vascular endothelial growth factor receptor.

(2014) Cell Biochem Biophys 70

PubMed: 25069724 | PubMedCentral: PMC4224745 | DOI: 10.1007/s12013-014-0151-x

This interaction view was created using the dimer complex structure of VEGF and VEGFR (PDB id: 1FLT).

Publication Year: 2014


Inhibition of VEGF: a novel mechanism to control angiogenesis by Withania somnifera's key metabolite Withaferin A.

(2013) In Silico Pharmacol 1

PubMed: 25505656 | PubMedCentral: PMC4230651 | DOI: 10.1186/2193-9616-1-11

Methods Ligand and receptor The crystal structure (1.7 Å resolution) of the VEGF in complex with domain 2 of the Flt-1 receptor [PDB: 1FLT], was obtained from the Protein Data Bank (PDB) (Berm... n et al.

Figure 1 Structural presentation of VEGF (PDB: 1FLT).

Publication Year: 2013