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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
3lmhADPMyosin heavy chain kinase A2.7.11.7

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3lmhADPMyosin heavy chain kinase A2.7.11.71.000
3llaACPMyosin heavy chain kinase A2.7.11.70.628
4zs4ATPMyosin heavy chain kinase A2.7.11.70.615
5e9eANPMyosin heavy chain kinase A2.7.11.70.611
4zmeADNMyosin heavy chain kinase A2.7.11.70.609
3pdtADPMyosin heavy chain kinase A2.7.11.70.558
1ia9ANPTransient receptor potential cation channel subfamily M member 72.7.11.10.532
3lmiATPMyosin heavy chain kinase A2.7.11.70.509
2wjoQUDBeta-secretase 13.4.23.460.507
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.498
1xorZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.496
5kf9ACOPredicted acetyltransferase/0.493
3rtnRTNBeta-secretase 13.4.23.460.490
3bjcWANcGMP-specific 3',5'-cyclic phosphodiesterase/0.489
4g2yNI5cGMP-specific 3',5'-cyclic phosphodiesterase/0.488
3ufl508Beta-secretase 13.4.23.460.487
3sn7540cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.486
4bbxLKFcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.485
1y2k7DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.481
2ouu35GcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.480
5kgjACOPredicted acetyltransferase/0.480
1y2c3DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.479
3d3p20AcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.479
3rsv3RSBeta-secretase 13.4.23.460.479
3sni546cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.479
4rh10TTSpore photoproduct lyase/0.479
5kf2ACOPredicted acetyltransferase/0.479
2owb626Serine/threonine-protein kinase PLK12.7.11.210.478
2y0jAXCcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.478
4oew5IOcGMP-specific 3',5'-cyclic phosphodiesterase/0.478
1zprCB3Thymidylate synthase/0.477
3o57ZG2cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.477
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.475
1udtVIAcGMP-specific 3',5'-cyclic phosphodiesterase/0.474
3d5wADPSerine/threonine-protein kinase PLK/0.474
4fcb0T7cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.474
5kgpACOPredicted acetyltransferase/0.474
2q153MRBeta-secretase 13.4.23.460.473
4oex5EOcGMP-specific 3',5'-cyclic phosphodiesterase/0.473
2a4nCOAAac(6')-Ii protein/0.472
2b8jADNClass B acid phosphatase3.1.3.20.472
3c36KAIGlutamate receptor ionotropic, kainate 1/0.472
3sl8JN7cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.472
2w5aADPSerine/threonine-protein kinase Nek22.7.11.10.471
4g2wNI0cGMP-specific 3',5'-cyclic phosphodiesterase/0.471
2yog74XThymidylate kinase/0.470
4fcd0T6cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.470
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.470
1n71COAAac(6')-Ii protein/0.469
3byzH11Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.469
3l5bBDOBeta-secretase 13.4.23.460.469
2ovyPFJcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.468
2vbpVB1Isopenicillin N synthase1.21.3.10.468
3pahXDEPhenylalanine-4-hydroxylase1.14.16.10.468
4a81DXCMajor pollen allergen Bet v 1-A/0.468
4hf415HcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.468
2o8h227cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.467
3uaxNOSPurine nucleoside phosphorylase DeoD-type/0.467
1pd9CO4Dihydrofolate reductase1.5.1.30.466
2in6839Wee1-like protein kinase2.7.10.20.466
3h4vNAPPteridine reductase 11.5.1.330.466
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.466
4ddl0JQcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.466
4heu15JcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.466
3aivHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase, chloroplastic3.2.1.1820.465
1tduDURThymidylate synthase/0.464
3qpoPFRcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.464
3rthRTHBeta-secretase 13.4.23.460.464
1bq1CB3Thymidylate synthase/0.463
2nnqT4BFatty acid-binding protein, adipocyte/0.463
3o56ZG1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.463
1fmjRTLRetinol dehydratase/0.462
1oc1ASVIsopenicillin N synthase1.21.3.10.461
1y2d4DEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.461
1z5uCMPClass B acid phosphatase/0.461
3v49PK0Androgen receptor/0.461
4u9yCOAAlpha-tubulin N-acetyltransferase 1/0.461
4u9zCOAAlpha-tubulin N-acetyltransferase 1/0.461
1uwhBAXSerine/threonine-protein kinase B-raf2.7.11.10.460
2jddACOProbable acetyltransferase/0.460
3bi6396Wee1-like protein kinase2.7.10.20.460
3ituIBMcGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.460
3rviRVIBeta-secretase 13.4.23.460.460
4iarERM5-hydroxytryptamine receptor 1B/0.460
2g1a5HGClass B acid phosphatase3.1.3.20.459
2jc6QPPCalcium/calmodulin-dependent protein kinase type 1D2.7.11.170.459
2z1xPRFQueuine tRNA-ribosyltransferase2.4.2.290.459
2z2w770Wee1-like protein kinase2.7.10.20.459
2azzTCHPhospholipase A2, major isoenzyme3.1.1.40.458
2xkc4VQSerine/threonine-protein kinase Nek22.7.11.10.458
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.458
2zwaSAHtRNA wybutosine-synthesizing protein 42.1.1.2900.457
3gi2GHWDihydrofolate reductase1.5.1.30.457
4ddrMMVDihydrofolate reductase1.5.1.30.457
4wbdADPPutative cysteine ligase BshC/0.457
2d3aADPGlutamine synthetase root isozyme 36.3.1.20.456
2mokFMNFlavodoxin 1/0.456
3sl2ATPSensor histidine kinase WalK/0.456
4ge40KEKynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.456
1b87ACOAac(6')-Ii protein/0.455
3qg2CP6Bifunctional dihydrofolate reductase-thymidylate synthase/0.455
4mvh2F5cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.455
1xomCIOcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.454
3ar4TG1Sarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.454
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
3qppPFWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.454
4ia05BBcGMP-specific 3',5'-cyclic phosphodiesterase/0.454
4muw2F4cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.454
5kf8ACOPredicted acetyltransferase/0.454
1bk0ACVIsopenicillin N synthase1.21.3.10.453
1crbRTLRetinol-binding protein 1/0.453
1s4eADPGalactokinase/0.453
1uaeUD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.453
1v35NAIEnoyl-ACP reductase/0.453
2pl0STITyrosine-protein kinase Lck2.7.10.20.453
2vd0D27Hematopoietic prostaglandin D synthase/0.453
3c35KAIGlutamate receptor ionotropic, kainate 1/0.453
3lakKR1Gag-Pol polyprotein2.7.7.490.453
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.453
1dgbNDPCatalase1.11.1.60.452
1nceCB3Thymidylate synthase/0.452
1x8b824Wee1-like protein kinase2.7.10.20.452
1xoqROFcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.452
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.452
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.452
3qpnPFKcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.452
3to3ATPPetrobactin biosynthesis protein AsbB/0.452
3uayADNPurine nucleoside phosphorylase DeoD-type/0.452
3zp4TSAChorismate mutase AroH5.4.99.50.452
5b1yNDP3-oxoacyl-[acyl-carrier-protein] reductase/0.452
1synF89Thymidylate synthase/0.451
1tbbROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.451
2f7x4EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.451
2p4iMR9Angiopoietin-1 receptor2.7.10.10.451
4a2aATPCell division protein FtsA/0.451
4gd9BTNStreptavidin/0.451
1w06W05Isopenicillin N synthase1.21.3.10.450
2ejzSAHDiphthine synthase/0.450
2ovmAS0Progesterone receptor/0.450
2rl52RLVascular endothelial growth factor receptor 22.7.10.10.450
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.450
3vi5M4MHematopoietic prostaglandin D synthase/0.450
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
1s9dAFBCytohesin-2/0.449
1s9dAFBADP-ribosylation factor 1/0.449
1sojIBMcGMP-inhibited 3',5'-cyclic phosphodiesterase B3.1.4.170.449
1trgCB3Thymidylate synthase/0.449
1xf0ASDAldo-keto reductase family 1 member C3/0.449
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.449
2wkyIBCGlutamate receptor ionotropic, kainate 1/0.449
2z3uCRRCytochrome P450/0.449
3aiqHBO4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1b, chloroplastic3.2.1.1820.449
3ntz3TZDihydrofolate reductase1.5.1.30.449
3tfjTHGDimethylsulfonioproprionate demethylase DmdA2.1.1.2690.449
3x2fNAIAdenosylhomocysteinase/0.449
4dbw511Aldo-keto reductase family 1 member C3/0.449
4j6cSTRCytochrome P450 monooxygenase/0.449
4tlaADPCircadian clock protein kinase KaiC2.7.11.10.449
5a0yCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.449
5a0yCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.449
1hfqMOTDihydrofolate reductase1.5.1.30.448
1jujLYAThymidylate synthase2.1.1.450.448
1rkpIBMcGMP-specific 3',5'-cyclic phosphodiesterase/0.448
2puiADPMethylthioribose kinase2.7.1.1000.448
3g4iD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
3gphOIDCytochrome P450 2E11.14.130.448
3tvxPNXcAMP-specific 3',5'-cyclic phosphodiesterase 4A3.1.4.530.448
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4lsaBLDProtein BRASSINOSTEROID INSENSITIVE 12.7.10.10.448
4pl9ADPEthylene receptor 1/0.448
4tzk641Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.448
1m67BOAGlycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal1.1.1.80.447
1tsdF89Thymidylate synthase/0.447
2fb8215Serine/threonine-protein kinase B-raf2.7.11.10.447
2ovvPFHcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
3af1GDPPantothenate kinase2.7.1.330.447
3d7zGK5Mitogen-activated protein kinase 14/0.447
3hv3R49Mitogen-activated protein kinase 14/0.447
3njoPYVAbscisic acid receptor PYR1/0.447
3nu03TUDihydrofolate reductase1.5.1.30.447
4fqsLYAThymidylate synthase ThyA/0.447
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.447
4nbwNADShort-chain dehydrogenase/reductase SDR/0.447
1dlsMTXDihydrofolate reductase1.5.1.30.446
1jdzFMBPurine nucleoside phosphorylase/0.446
1s2cFLFAldo-keto reductase family 1 member C3/0.446
1zklIBMHigh affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7A3.1.4.530.446
2j7cIDEBeta-glucosidase A3.2.1.210.446
3cobADPKinesin heavy chain-like protein/0.446
3g4gD71cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
3sl6JN8cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.446
3um81CYBifunctional dihydrofolate reductase-thymidylate synthase/0.446
3vweCOAAlpha-tubulin N-acetyltransferase 1/0.446
4c1iEH9cGMP-dependent 3',5'-cyclic phosphodiesterase3.1.4.170.446
4ckrDI1Epithelial discoidin domain-containing receptor 12.7.10.10.446
1mlzPLPAdenosylmethionine-8-amino-7-oxononanoate aminotransferase2.6.1.620.445
2ourCMPcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.445
2ym1FADPhenylacetone monooxygenase1.14.13.920.445
3up3XCAaceDAF-12/0.445
4epq0RRPoly(ADP-ribose) glycohydrolase/0.445
4f1mACPProbable serine/threonine-protein kinase roco42.7.11.10.445
4zasTYDCalS13/0.445
1t7o152Carnitine O-acetyltransferase2.3.1.70.444
2vt4P32Beta-1 adrenergic receptor/0.444
3qyw6PBMitogen-activated protein kinase 12.7.11.240.444
4bfxZVXPantothenate kinase2.7.1.330.444
4pnmNU1Tankyrase-22.4.2.300.444
5ds309LPoly [ADP-ribose] polymerase 12.4.2.300.444
1c1c612Gag-Pol polyprotein2.7.7.490.443
1h36R88Squalene--hopene cyclase4.2.1.1290.443
1rszDIHPurine nucleoside phosphorylase2.4.2.10.443
1zknIBMcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.443
2bfmTOPPteridine reductase 11.5.1.330.443
2ea1GPGRibonuclease I3.1.27.60.443
2j0sANPEukaryotic initiation factor 4A-III3.6.4.130.443
2zu9GDPMannosyl-3-phosphoglycerate synthase2.4.1.2170.443
3n87N873-dehydroquinate dehydratase4.2.1.100.443
3ox34X4Ribosyldihydronicotinamide dehydrogenase [quinone]/0.443
4acuQN7Beta-secretase 13.4.23.460.443
4dch4DCGlucokinase2.7.1.20.443
4eyb0WOMetallo-beta-lactamase type 2/0.443
5c6cCMPcGMP-dependent protein kinase 22.7.11.120.443
2ycxP32Beta-1 adrenergic receptor/0.443
1aj22PHDihydropteroate synthase/0.442
1d4dFADFumarate reductase flavoprotein subunit1.3.5.40.442
1jtuLYBThymidylate synthase/0.442
1v08NTZ4-hydroxy-7-methoxy-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-2-yl glucoside beta-D-glucosidase 1, chloroplastic3.2.1.1820.442
1x8lOXRRetinol dehydratase/0.442
2yeiXQIHeat shock protein HSP 90-alpha/0.442
3arpDEQChitinase A/0.442
3fr5I4AFatty acid-binding protein, adipocyte/0.442
3m1vCOMMethyl-coenzyme M reductase I subunit alpha2.8.4.10.442
3m1vCOMMethyl-coenzyme M reductase I subunit beta2.8.4.10.442
3zkyWT4Isopenicillin N synthase1.21.3.10.442
4fgj1PQRibosyldihydronicotinamide dehydrogenase [quinone]/0.442
4fk3325Serine/threonine-protein kinase B-raf2.7.11.10.442
4glx0XSDNA ligase6.5.1.20.442
4hkfACOAlpha-tubulin N-acetyltransferase 1/0.442
1dggNDPCatalase1.11.1.60.441
1dr2TAPDihydrofolate reductase1.5.1.30.441
1mvsDTMDihydrofolate reductase1.5.1.30.441
1ozqPRFQueuine tRNA-ribosyltransferase2.4.2.290.441
2jbsFMNp-hydroxyphenylacetate 3-hydroxylase, oxygenase component/0.441
2y035FWBeta-1 adrenergic receptor/0.441
3fcoIIGCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
3gcq1BUMitogen-activated protein kinase 14/0.441
3ns2PYVAbscisic acid receptor PYL2/0.441
3prfFP3Serine/threonine-protein kinase B-raf2.7.11.10.441
3u3o3QVSulfotransferase 1A12.8.2.10.441
3zkuHCVIsopenicillin N synthase1.21.3.10.441
4h6rFDAProline dehydrogenase/0.441
4je5PLPAromatic/aminoadipate aminotransferase 12.6.1.390.441
4tjy3GNTankyrase-22.4.2.300.441
4wa9AXITyrosine-protein kinase ABL12.7.10.20.441
1dr5NAPDihydrofolate reductase1.5.1.30.440
1f4fTP3Thymidylate synthase/0.440
1jtqLY3Thymidylate synthase/0.440
1sd2MTHS-methyl-5'-thioadenosine phosphorylase/0.440
1zisINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.440
2bbqPFGThymidylate synthase/0.440
2jdcCAOProbable acetyltransferase/0.440
2pbwDOQGlutamate receptor ionotropic, kainate 1/0.440
2wd8VGFPteridine reductase/0.440
2wgs1AZGlutamine synthetase6.3.1.20.440
3djlFADPutative acyl-CoA dehydrogenase AidB1.3.990.440
3pg3DG7Mitogen-activated protein kinase 14/0.440
3qh23NMThiazole tautomerase/0.440
4gts7TPGeranylgeranyl transferase type-2 subunit beta2.5.1.600.440
4hvb19PPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4yfy0FXVioF/0.440