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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
2rtgBTNStreptavidin

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
2rtgBTNStreptavidin/1.000
2izgBTNStreptavidin/0.770
2izlIMIStreptavidin/0.724
2rtdBTNStreptavidin/0.723
2izhBTNStreptavidin/0.711
2rtiGLLStreptavidin/0.709
2rteBTNStreptavidin/0.694
2rtfBTNStreptavidin/0.693
2izfBTNStreptavidin/0.680
1sreHABStreptavidin/0.656
1lcwSHMStreptavidin/0.654
2rtoIMIStreptavidin/0.652
2rtpIMIStreptavidin/0.649
1i9hBNIStreptavidin/0.647
3ry2BTNStreptavidin/0.644
2c4iBTNAvidin/0.641
4gdaBTNStreptavidin/0.639
1mk5BTNStreptavidin/0.638
1stpBTNStreptavidin/0.634
4bx7B4FStreptavidin/0.630
2rtnIMIStreptavidin/0.623
2rtrIMIStreptavidin/0.619
1sriDMBStreptavidin/0.617
1srgMHBStreptavidin/0.615
3wyqBTNStreptavidin/0.614
4dneDTBStreptavidin/0.614
3wznBTNStreptavidin/0.612
1srhMOBStreptavidin/0.610
1srjNABStreptavidin/0.610
2y3fBTNStreptavidin/0.606
2fhnBNIAvidin-related protein 4/5/0.604
1df8BTNStreptavidin/0.603
1rxhBNIStreptavidin/0.599
1swtBTNStreptavidin/0.599
1y52BTNAvidin-related protein 4/5/0.593
1srfMTBStreptavidin/0.592
1luqBTNStreptavidin/0.588
2rtqIMIStreptavidin/0.586
1lczBH7Streptavidin/0.583
2izkGLLStreptavidin/0.582
2uz2BTNAvd protein/0.572
2rtkGLLStreptavidin/0.570
4z28BTNHoefavidin/0.561
3rdqDTBStreptavidin/0.555
2aviBTNAvidin/0.554
1avdBTNAvidin/0.553
2iziBTNStreptavidin/0.552
2izjBTNStreptavidin/0.552
2uywBTNAvd protein/0.552
3ew2BTNHypothetical conserved protein/0.550
3t2wBTNAvidin/streptavidin/0.546
2fhlBNIAvidin-related protein 4/5/0.545
1swpBTQStreptavidin/0.543
1nc9IMIStreptavidin/0.539
1swpBTNStreptavidin/0.539
4bcsBTNAvidin-related protein 4/5/0.534
1sweBTNStreptavidin/0.526
2rtmIMIStreptavidin/0.525
1n9mBTNStreptavidin/0.524
4gd9BTNStreptavidin/0.519
1ndjBTNStreptavidin/0.517
1swnBTNStreptavidin/0.516
2zscBTNTamavidin2/0.516
3pahXDEPhenylalanine-4-hydroxylase1.14.16.10.505
5pahLDPPhenylalanine-4-hydroxylase1.14.16.10.503
1mepBTNStreptavidin/0.501
2a5c8DAAvidin/0.497
4yvbBTNStreptavidin/0.492
4pahLNRPhenylalanine-4-hydroxylase1.14.16.10.491
2rtlIMIStreptavidin/0.488
2jgsBTNAvidin/0.484
1nceCB3Thymidylate synthase/0.483
1c3x8IGPurine nucleoside phosphorylase2.4.2.10.482
2xlpFADPutative flavin-containing monooxygenase/0.480
3h4vDVPPteridine reductase 11.5.1.330.480
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.479
4bj8BTNAvidin/0.479
4eplJAIJasmonic acid-amido synthetase JAR16.3.20.479
1swdBTNStreptavidin/0.478
3hmvHBTcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.478
1e2nRCAThymidine kinase/0.476
2xlrFADPutative flavin-containing monooxygenase/0.476
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.475
1ndhFADNADH-cytochrome b5 reductase 31.6.2.20.474
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.472
2tohHBITyrosine 3-monooxygenase1.14.16.20.471
3up0D7SaceDAF-12/0.471
1piwNAPNADP-dependent alcohol dehydrogenase 61.1.1.20.470
2fznFADBifunctional protein PutA1.5.5.20.469
3aiqHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic3.2.1.1820.469
3wypBSOStreptavidin/0.469
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.469
5iqeGNPBifunctional AAC/APH2.3.10.469
1mabADPATP synthase subunit beta, mitochondrial3.6.3.140.468
2zbaZBATrichothecene 3-O-acetyltransferase/0.468
1ib0FADNADH-cytochrome b5 reductase 31.6.2.20.467
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.467
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.467
1trgCB3Thymidylate synthase/0.466
3nx2FERFerulic acid decarboxylase/0.466
1dnaCB3Thymidylate synthase/0.465
3bw2FMNPutative 2-nitropropane dioxygenase/0.465
3c3xNAPEugenol synthase 11.1.1.3180.465
3e2sFADBifunctional protein PutA1.5.5.20.465
1jtqLY3Thymidylate synthase/0.464
3d4bDZDNAD-dependent protein deacetylase/0.464
3pqbVGPPutative oxidoreductase/0.464
3bw4FMNPutative 2-nitropropane dioxygenase/0.463
1ja0NAPNADPH--cytochrome P450 reductase/0.462
2ovvPFHcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.462
4psbGA3Cytokinin-specific binding protein/0.462
3sn6P0GBeta-2 adrenergic receptor/0.462
4xd1T3QQdtf/0.461
1e92HBIPteridine reductase 11.5.1.330.460
1nw6SFGModification methylase RsrI2.1.1.720.460
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.460
4xczT3QQdtf/0.460
1thnADPAnti-sigma F factor/0.459
2fzjDH3Dihydrofolate reductase1.5.1.30.459
3tvxPNXcAMP-specific 3',5'-cyclic phosphodiesterase 4A3.1.4.530.459
2r6jNDPEugenol synthase 11.1.1.3180.458
4cdmFO1Deoxyribodipyrimidine photolyase/0.458
1mvsDTMDihydrofolate reductase1.5.1.30.457
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.457
3nwlNDPCatalase1.11.1.60.457
1hvyD16Thymidylate synthase2.1.1.450.456
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.456
2bf7HBIPteridine reductase 11.5.1.330.456
2x9dITCTetracycline repressor protein class D/0.456
4qzuRTLRetinol-binding protein 2/0.456
1axwMTXThymidylate synthase/0.455
2zi63D1Deoxycytidine kinase2.7.1.740.455
3elm24FCollagenase 33.4.240.455
1fwkADPHomoserine kinase2.7.1.390.454
1j3kWRABifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.454
1obnASVIsopenicillin N synthase1.21.3.10.454
1tkaN3TTransketolase 12.2.1.10.454
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
2qtaTDPPyruvate dehydrogenase E1 component1.2.4.10.454
3arqDM5Chitinase A/0.454
3biy01KHistone acetyltransferase p300/0.454
3wg6NDPNADPH-dependent conjugated polyketone reductase C1/0.454
4dz7D02Carbonic anhydrase 24.2.1.10.454
4kxjP34Nucleoprotein/0.454
1h35R01Squalene--hopene cyclase4.2.1.1290.453
1lqaNDPProtein tas/0.453
1ly4COQDihydrofolate reductase1.5.1.30.453
2f4jVX6Tyrosine-protein kinase ABL12.7.10.20.453
2h94FADLysine-specific histone demethylase 1A10.453
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.453
4b1iA8PPoly(ADP-ribose) glycohydrolase3.2.1.1430.453
2ftoCB3Thymidylate synthase/0.452
2weyEV1cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
3ch6311Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.452
3dopNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.452
3gyuDL7Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.452
3pjcPJCTyrosine-protein kinase JAK32.7.10.20.452
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.452
4j6dTESCytochrome P450 monooxygenase/0.452
4oex5EOcGMP-specific 3',5'-cyclic phosphodiesterase/0.452
1kt6RTLRetinol-binding protein 4/0.451
1r2jFADFkbI/0.451
2vqbFADPutative flavin-containing monooxygenase/0.451
2wmdZZ0NmrA-like family domain-containing protein 1/0.451
2zjwREFCasein kinase II subunit alpha2.7.11.10.451
4at3LTIBDNF/NT-3 growth factors receptor2.7.10.10.451
4f32N323-oxoacyl-[acyl-carrier-protein] synthase 2/0.451
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.451
4gevCB3Thymidylate synthase/0.451
4yddMD1DMSO reductase family type II enzyme, molybdopterin subunit/0.451
1jtuLYBThymidylate synthase/0.450
1xonPILcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.450
2wo7ASVIsopenicillin N synthase1.21.3.10.450
3bv7NAP3-oxo-5-beta-steroid 4-dehydrogenase/0.450
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.450
4ajm3A6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.450
5iqbGNPBifunctional AAC/APH2.3.10.450
1h69ARHNAD(P)H dehydrogenase [quinone] 11.6.5.20.449
1tduDURThymidylate synthase/0.449
1wsvTHHAminomethyltransferase, mitochondrial/0.449
3negPYVAbscisic acid receptor PYL1/0.449
3nguADPNucleoside diphosphate kinase/0.449
4fcd0T6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.449
4imoPWZProstaglandin-H2 D-isomerase5.3.99.20.449
1lkeDOGBilin-binding protein/0.448
1ycgFMNNitric oxide reductase10.448
3a25SAMtRNA(Phe) (4-demethylwyosine(37)-C(7)) aminocarboxypropyltransferase/0.448
4l64C2F5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase2.1.1.140.448
1gveNAPAflatoxin B1 aldehyde reductase member 310.447
1kceCB3Thymidylate synthase/0.447
1tl7ONMAdenylate cyclase type 2/0.447
1tl7ONMAdenylate cyclase type 5/0.447
1zdwFLVPrenyltransferase/0.447
2plaNADGlycerol-3-phosphate dehydrogenase 1-like protein/0.447
2y0jAXCcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
3bi6396Wee1-like protein kinase2.7.10.20.447
3pz23PZGeranylgeranyl transferase type-2 subunit beta2.5.1.600.447
3qpoPFRcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
4a8v2ANMajor pollen allergen Bet v 1-J/0.447
1blzACVIsopenicillin N synthase1.21.3.10.446
1hniAAAGag-Pol polyprotein2.7.7.490.446
1jpaANPEphrin type-B receptor 22.7.10.10.446
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
2kceD16Thymidylate synthase/0.446
3bgsDIHPurine nucleoside phosphorylase2.4.2.10.446
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.446
5iqgGDPBifunctional AAC/APH2.3.10.446
7catNDPCatalase1.11.1.60.446
1j9zFADNADPH--cytochrome P450 reductase/0.445
1kziTHGThymidylate synthase/0.445
1mrqSTRAldo-keto reductase family 1 member C1/0.445
1osvCHCBile acid receptor/0.445
1rszDIHPurine nucleoside phosphorylase2.4.2.10.445
1s7gNADNAD-dependent protein deacylase 2/0.445
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.445
2ouyCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
3qeoLLTDeoxycytidine kinase2.7.1.740.445
4dpdDHFBifunctional dihydrofolate reductase-thymidylate synthase/0.445
4j6cSTRCytochrome P450 monooxygenase/0.445
4mr92BXGamma-aminobutyric acid type B receptor subunit 1/0.445
4mryCEIObelin/0.445
4ug91EWNitric oxide synthase oxygenase1.14.13.1650.445
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.445
1dgbNDPCatalase1.11.1.60.444
1lnmDTXBilin-binding protein/0.444
1mvtDTMDihydrofolate reductase1.5.1.30.444
1qyxASDEstradiol 17-beta-dehydrogenase 11.1.1.620.444
3mpiFADGlutaryl-CoA dehydrogenase1.3.99.320.444
4ajdF04cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.444
1hb1OCVIsopenicillin N synthase1.21.3.10.443
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.443
2mjpANPdITP/XTP pyrophosphatase3.6.1.190.443
2oegUPGUDP-glucose pyrophosphorylase/0.443
2op18PCEnoyl-ACP reductase/0.443
2wufKEM4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase3.7.1.170.443
3h3sH15Collagen type IV alpha-3-binding protein/0.443
3vfqAR6Poly [ADP-ribose] polymerase 142.4.2.300.443
4d86ADPPoly [ADP-ribose] polymerase 142.4.2.300.443
4jlj1NMDeoxycytidine kinase2.7.1.740.443
4jlm1NNDeoxycytidine kinase2.7.1.740.443
4pnmNU1Tankyrase-22.4.2.300.443
3qakUKAAdenosine receptor A2a/0.443
1ldqSHMAvidin/0.442
1siqFADGlutaryl-CoA dehydrogenase, mitochondrial1.3.8.60.442
2ftoTMPThymidylate synthase/0.442
3hxdBD7Geranylgeranyl transferase type-2 subunit beta2.5.1.600.442
3lakKR1Gag-Pol polyprotein2.7.7.490.442
4knzCB3Thymidylate synthase/0.442
4z3dNDPCarbonyl reductase [NADPH] 11.1.1.1840.442
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
1jtvTESEstradiol 17-beta-dehydrogenase 11.1.1.620.441
1oc1ASVIsopenicillin N synthase1.21.3.10.441
1rejB1LcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.441
2hzqSTRApolipoprotein D/0.441
2pk3A2RGDP-6-deoxy-D-mannose reductase/0.441
2pksG44Prothrombin3.4.21.50.441
2qw8NAPEugenol synthase 11.1.1.3180.441
2qx7NAPEugenol synthase 11.1.1.3180.441
3anlSYC1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.441
3arvSAUChitinase A/0.441
3c3dFO12-phospho-L-lactate transferase/0.441
3dds26BGlycogen phosphorylase, liver form2.4.1.10.441
3el7PD3Proto-oncogene tyrosine-protein kinase Src2.7.10.20.441
3exfTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.441
3exfTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.441
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.441
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.441
3mb714ICasein kinase II subunit alpha2.7.11.10.441
3vf60H6Glucokinase2.7.1.20.441
4bcaFADAlkyldihydroxyacetonephosphate synthase, peroxisomal2.5.1.260.441
5p2pDHGPhospholipase A2, major isoenzyme3.1.1.40.441
1dorFMNDihydroorotate dehydrogenase A (fumarate)1.3.98.10.440
1s3uTQDDihydrofolate reductase1.5.1.30.440
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.440
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.440
2jdvL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.440
2zi53L1Deoxycytidine kinase2.7.1.740.440
3cth319Hepatocyte growth factor receptor2.7.10.10.440
3koo24DBifunctional epoxide hydrolase 23.3.2.100.440
4rrfA3SThreonine--tRNA ligase6.1.1.30.440
4xo7NAPAldo-keto reductase family 1 member C2/0.440
8catNDPCatalase1.11.1.60.440