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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Cavity similarities measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Cavities are compared using Shaper.
For more information, please see the following publication: Desaphy J. et al. Comparison and Druggability Prediction of protein-Ligand Binding sites from pharmacophore-annotated cavity shapes J. Chem. Inf. Model., 2012, 52(8), pp2287-2299

Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3jqcJU2Pteridine reductase, putative

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
3jqcJU2Pteridine reductase, putative/1.000
2x9vTMQPteridine reductase/0.626
1p33MTXPteridine reductase 11.5.1.330.611
3jq8DX3Pteridine reductase, putative/0.604
2x9nAX3Pteridine reductase/0.593
2yhuWHFPteridine reductase/0.583
2vz0D64Pteridine reductase/0.581
3jq9AX1Pteridine reductase, putative/0.564
2wd7VGDPteridine reductase/0.555
3jqgAX6Pteridine reductase, putative/0.553
2bfmTOPPteridine reductase 11.5.1.330.548
3jq7DX2Pteridine reductase, putative/0.543
3bmnAX3Pteridine reductase/0.537
3bmcFOLPteridine reductase/0.534
3h4vDVPPteridine reductase 11.5.1.330.525
3jqbDX6Pteridine reductase, putative/0.525
1mxfMTXPutative pteridine reductase 2/0.516
3mcvMCVPteridine reductase/0.510
1e92HBIPteridine reductase 11.5.1.330.508
2bfpH4BPteridine reductase 11.5.1.330.507
3bmqAX5Pteridine reductase/0.502
3biz61EWee1-like protein kinase2.7.10.20.501
3jq6DX1Pteridine reductase, putative/0.501
2bfaCB3Pteridine reductase 11.5.1.330.493
2bf7HBIPteridine reductase 11.5.1.330.490
1zq5E04Aldo-keto reductase family 1 member C3/0.488
3p9tTCLRepressor/0.482
1x2hLPALipoate-protein ligase A6.3.1.200.478
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.478
5uviZMAAdenosine receptor A2a/0.478
3k47D09Dihydrofolate reductase1.5.1.30.477
1dlsMTXDihydrofolate reductase1.5.1.30.475
5k2aZMAAdenosine receptor A2a/0.474
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.473
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.473
1s3wTQTDihydrofolate reductase1.5.1.30.471
4ey6GNTAcetylcholinesterase3.1.1.70.471
2yac937Serine/threonine-protein kinase PLK12.7.11.210.470
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.469
1zknIBMcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.469
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.469
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.468
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.467
2z2w770Wee1-like protein kinase2.7.10.20.467
1giqNAIIota toxin component Ia/0.466
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.465
1el4CTZObelin/0.464
1hfrMOTDihydrofolate reductase1.5.1.30.464
1yw8A75Methionine aminopeptidase 2/0.464
3o56ZG1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.464
4xt8TMQPossible bifunctional enzyme riboflavin biosynthesis protein RibD: diaminohydroxyphosphoribosylaminopyrimidine deaminase (Riboflavin-specific deaminase) + 5-amino-6-(5-phosphoribosylamino)uracil reduc/0.464
2in6839Wee1-like protein kinase2.7.10.20.463
3arpDEQChitinase A/0.463
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.463
3nxvD2FDihydrofolate reductase1.5.1.30.463
3pblETQD(3) dopamine receptor/0.463
1dr4HBIDihydrofolate reductase1.5.1.30.462
1frbZSTAldose reductase-related protein 2/0.462
3iakEV1cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.462
3r94FLRAldo-keto reductase family 1 member C3/0.461
5iu4ZMAAdenosine receptor A2a/0.461
5k2cZMAAdenosine receptor A2a/0.461
3emlZMAAdenosine receptor A2a/0.461
4a959MTGlycylpeptide N-tetradecanoyltransferase/0.460
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.460
4zqcF6FTryptophan synthase alpha chain/0.460
3h3qH13Collagen type IV alpha-3-binding protein/0.459
4jv41ORcAMP-dependent protein kinase type I-alpha regulatory subunit/0.459
3arvSAUChitinase A/0.458
1ry0PG2Aldo-keto reductase family 1 member C3/0.456
3lq4TDPPyruvate dehydrogenase E1 component1.2.4.10.456
3r6iJMSAldo-keto reductase family 1 member C3/0.456
1ro6ROLcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.455
3g58988cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.455
3njoPYVAbscisic acid receptor PYR1/0.455
1y60H4M5,6,7,8-tetrahydromethanopterin hydro-lyase4.2.1.1470.454
3cr0809Wee1-like protein kinase2.7.10.20.454
3exfTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.454
3exfTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.454
4eilFOLBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.454
4fcd0T6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.454
4gqkADPActin cross-linking toxin VgrG1/0.454
1tbbROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.453
2wd8VGFPteridine reductase/0.453
4i6h1C8Serine/threonine-protein kinase PLK22.7.11.210.453
1q0rAKTAclacinomycin methylesterase RdmC3.1.1.950.452
1ve3SAMUncharacterized protein/0.451
2d06ESTSulfotransferase 1A12.8.2.10.451
3hl0NADMaleylacetate reductase/0.451
4kd79DRDihydrofolate reductase1.5.1.30.451
4muw2F4cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.451
5k2bZMAAdenosine receptor A2a/0.451
5jtbZMAAdenosine receptor A2a/0.451
1dlrMXADihydrofolate reductase1.5.1.30.450
1uhjCZBAequorin-2/0.450
2xtbKRMAdenosine kinase, putative/0.450
3o57ZG2cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.450
4i6f1C7Serine/threonine-protein kinase PLK22.7.11.210.450
1db56INPhospholipase A2, membrane associated/0.449
1e7wMTXPteridine reductase 11.5.1.330.449
1pd8CO4Dihydrofolate reductase1.5.1.30.449
1pr4MTPPurine nucleoside phosphorylase DeoD-type/0.449
1upw444Oxysterols receptor LXR-beta/0.449
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
1zgcA2EAcetylcholinesterase3.1.1.70.449
2bxoOPBSerum albumin/0.449
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.449
3bloQEIQueuine tRNA-ribosyltransferase2.4.2.290.449
3c34KAIGlutamate receptor ionotropic, kainate 1/0.449
3k4s0MOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
3r43ID8Aldo-keto reductase family 1 member C3/0.449
4bfwZVWPantothenate kinase2.7.1.330.449
2po7CHDFerrochelatase, mitochondrial4.99.1.10.448
1q9mROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
2ewaSB2Mitogen-activated protein kinase 14/0.447
2gqg1N1Tyrosine-protein kinase ABL12.7.10.20.447
3d2dRENReticuline oxidase1.21.3.30.447
3gyf51PDihydrofolate reductase1.5.1.30.447
4kbn25UDihydrofolate reductase1.5.1.30.447
1o6qR17Squalene--hopene cyclase4.2.1.1290.446
1xf0ASDAldo-keto reductase family 1 member C3/0.446
1yhoTRRDihydrofolate reductase1.5.1.30.446
3gcq1BUMitogen-activated protein kinase 14/0.446
4pnmNU1Tankyrase-22.4.2.300.446
1jf2CZHObelin/0.445
2ejzSAHDiphthine synthase/0.445
2f3815MAldo-keto reductase family 1 member C3/0.445
3up3XCAaceDAF-12/0.445
1oynROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.444
2ea4F79Methionine aminopeptidase 2/0.444
3dh7FMNIsopentenyl-diphosphate delta-isomerase/0.444
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.444
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.444
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.443
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.443
4rh10TTSpore photoproduct lyase/0.443
4z87GDPInosine-5'-monophosphate dehydrogenase/0.443
5iua6DXAdenosine receptor A2a/0.443
1jdzFMBPurine nucleoside phosphorylase/0.442
1l8qADPChromosomal replication initiator protein DnaA/0.442
1synF89Thymidylate synthase/0.442
4a4o664Serine/threonine-protein kinase PLK12.7.11.210.442
4dkbDUNDeoxyuridine triphosphatase, putative/0.442
4iarERM5-hydroxytryptamine receptor 1B/0.442
1d3dBZTProthrombin3.4.21.50.441
1paxDHQPoly [ADP-ribose] polymerase 12.4.2.300.441
2fzjDH3Dihydrofolate reductase1.5.1.30.441
2z7gEH9Adenosine deaminase3.5.4.40.441
3nj0PYVAbscisic acid receptor PYL2/0.441
4a4xJUPSerine/threonine-protein kinase Nek22.7.11.10.441
4gts7TPGeranylgeranyl transferase type-2 subunit beta2.5.1.600.441
1c7oPPGHemolysin/0.440
1rgsCMPcAMP-dependent protein kinase type I-alpha regulatory subunit/0.440
2io6330Wee1-like protein kinase2.7.10.20.440
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.440
2pl0STITyrosine-protein kinase Lck2.7.10.20.440
3h3t16HCollagen type IV alpha-3-binding protein/0.440
3nxtD2EDihydrofolate reductase1.5.1.30.440
4a33PS8Glycylpeptide N-tetradecanoyltransferase/0.440
4b6l9ZPSerine/threonine-protein kinase PLK32.7.11.210.440
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.440
4hmn16JAldo-keto reductase family 1 member C3/0.440
4n1fCZHObelin/0.440