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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
3vhe42QVascular endothelial growth factor receptor 22.7.10.1

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity
Align
3vhe42QVascular endothelial growth factor receptor 22.7.10.11.000
3wzeBAXVascular endothelial growth factor receptor 22.7.10.10.603
4asdBAXVascular endothelial growth factor receptor 22.7.10.10.590
3p7bP7BMitogen-activated protein kinase 14/0.561
5hidB1ESerine/threonine-protein kinase B-raf2.7.11.10.555
2e2b406Tyrosine-protein kinase ABL12.7.10.20.550
1kv1BMUMitogen-activated protein kinase 14/0.546
4hw764MMacrophage colony-stimulating factor 1 receptor2.7.10.10.541
3hv6R39Mitogen-activated protein kinase 14/0.531
3ugc046Tyrosine-protein kinase JAK2/0.528
2yisYISMitogen-activated protein kinase 14/0.525
3p5kP5KMitogen-activated protein kinase 14/0.525
3p7cP7CMitogen-activated protein kinase 14/0.523
1wbvLI3Mitogen-activated protein kinase 14/0.521
3gcuR48Mitogen-activated protein kinase 14/0.520
3hv5R24Mitogen-activated protein kinase 14/0.520
4r7iSTIMacrophage colony-stimulating factor 1 receptor2.7.10.10.520
3p78P78Mitogen-activated protein kinase 14/0.517
1kv2B96Mitogen-activated protein kinase 14/0.516
3p7aP7AMitogen-activated protein kinase 14/0.513
1wbnL09Mitogen-activated protein kinase 14/0.512
1wbsLI2Mitogen-activated protein kinase 14/0.512
2puuG2GMitogen-activated protein kinase 14/0.510
3d83GK6Mitogen-activated protein kinase 14/0.509
3cs9NILTyrosine-protein kinase ABL12.7.10.20.507
2hiw7MPTyrosine-protein kinase ABL12.7.10.20.506
3nnxEDDMitogen-activated protein kinase 14/0.506
3t54ATPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.506
3gcvSS6Mitogen-activated protein kinase 14/0.503
4h1m0YJProtein-tyrosine kinase 2-beta2.7.10.20.501
3nnwEDDMitogen-activated protein kinase 14/0.500
1c6yMK1Protease/0.499
2hznKINTyrosine-protein kinase ABL12.7.10.20.499
3hv71AUMitogen-activated protein kinase 14/0.499
3gi3B10Mitogen-activated protein kinase 14/0.497
3o8uBMUMitogen-activated protein kinase 14/0.497
3p79P79Mitogen-activated protein kinase 14/0.494
2qhcAB1Protease/0.490
1wbtWBTMitogen-activated protein kinase 14/0.488
3uvr06FMitogen-activated protein kinase 14/0.488
2izrBRKCasein kinase I isoform gamma-32.7.11.10.485
3aidARQGag-Pol polyprotein3.4.23.160.483
1bx6BA1cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.482
3nnuEDBMitogen-activated protein kinase 14/0.482
4b1vLABActin, alpha skeletal muscle/0.482
2uw6GVOcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.481
2uzuL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.480
3vid4TTVascular endothelial growth factor receptor 22.7.10.10.478
1xl2189Gag-Pol polyprotein3.4.23.160.477
1k6pXN3Gag-Pol polyprotein3.4.23.160.476
1w82L10Mitogen-activated protein kinase 14/0.476
2yiwYIWMitogen-activated protein kinase 14/0.476
3v04V04Dual specificity mitogen-activated protein kinase kinase 12.7.12.20.476
1npa3NHGag-Pol polyprotein3.4.23.160.475
1npwLGZGag-Pol polyprotein3.4.23.160.475
3k3jF4CMitogen-activated protein kinase 14/0.475
4z34ON7Lysophosphatidic acid receptor 1/0.475
3iodA6DPantothenate synthetase6.3.2.10.474
4nzoANPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.474
1t7i017Gag-Pol polyprotein3.4.23.160.473
2hc0AB2Protease/0.473
3gvuSTIAbelson tyrosine-protein kinase 22.7.10.20.473
3oogYTPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.473
4u03GTPCyclic GMP-AMP synthase/0.472
2hz0GINTyrosine-protein kinase ABL12.7.10.20.471
4a6bQG8Gag-Pol polyprotein3.4.23.160.471
1wbk568Pol protein/0.470
3qw2NADMyo-inositol-1-phosphate synthase (Ino1)/0.470
4k4p3TLGag-Pol polyprotein/0.470
3npcB96Mitogen-activated protein kinase 92.7.11.240.469
4hla017Gag-Pol polyprotein3.4.23.160.469
2oiqSTIProto-oncogene tyrosine-protein kinase Src2.7.10.20.468
1k6tXN1Gag-Pol polyprotein3.4.23.160.467
1v0pPVBCell division control protein 2 homolog2.7.11.220.467
3e8eG98cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.467
3livE16Protease/0.467
1w2xRCPAcetyl-CoA carboxylase/0.466
3litE15Protease/0.466
4l8mF46Mitogen-activated protein kinase 14/0.466
1k2b0Q4Gag-Pol polyprotein3.4.23.160.465
3imeBZ2Pantothenate synthetase6.3.2.10.465
3iocA5DPantothenate synthetase6.3.2.10.465
3v013V0Dual specificity mitogen-activated protein kinase kinase 12.7.12.20.465
1hpoUNIGag-Pol polyprotein3.4.23.160.464
1q8wM77cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.464
1vyzN5BCyclin-dependent kinase 22.7.11.220.464
2hmaSAMtRNA-specific 2-thiouridylase MnmA/0.464
2pym1UNGag-Pol polyprotein3.4.23.160.464
3hv4L51Mitogen-activated protein kinase 14/0.464
4bdgP3JSerine/threonine-protein kinase Chk22.7.11.10.464
1h1s4SPCyclin-dependent kinase 22.7.11.220.463
1osfKOSHeat shock protein HSP 90-alpha/0.463
1yetGDMHeat shock protein HSP 90-alpha/0.463
2pv7NADT-protein1.3.1.120.463
3tkuM77Serine/threonine-protein kinase MRCK beta2.7.11.10.463
4a6cQG9Gag-Pol polyprotein3.4.23.160.463
2vo7M05cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.462
3a99ANPSerine/threonine-protein kinase pim-12.7.11.10.462
3bwjARXcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.462
4eon1ROCyclin-dependent kinase 22.7.11.220.462
3dneLL1cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.461
5dulNDP1-deoxy-D-xylulose 5-phosphate reductoisomerase/0.461
3dy71CXDual specificity mitogen-activated protein kinase kinase 12.7.12.20.460
3ec0GRLGag-Pol polyprotein3.4.23.470.460
3o9aK14Pol polyprotein/0.460
3t99ADPInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2/0.460
3zptM8YGag-Pol polyprotein3.4.23.160.460
1hsgMK1Gag-Pol polyprotein/0.459
1w5vBE3Gag-Pol polyprotein3.4.23.160.459
1zp9ATPRIO-type serine/threonine-protein kinase Rio12.7.11.10.459
2gnhH52cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.459
2i4xKGQProtease/0.459
2oh02PYcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.459
2r64740Cyclin-dependent kinase 22.7.11.220.459
3cqwCQWRAC-alpha serine/threonine-protein kinase2.7.11.10.459
3ekt017Gag-Pol polyprotein3.4.23.160.459
3qxoX65Cyclin-dependent kinase 22.7.11.220.459
3r9hZ67Cyclin-dependent kinase 22.7.11.220.459
3s43478Protease/0.459
4asf62UATP-dependent molecular chaperone HSP82/0.459
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.459
4yryFADGlutamate synthase, beta subunit/0.459
1ec0BEDGag-Pol polyprotein3.4.23.160.458
1mrxK57Gag-Pol polyprotein3.4.23.160.458
2acxANPG protein-coupled receptor kinase 62.7.11.160.458
3nu3478Gag-Pol polyprotein3.4.23.160.458
3zpuM8BGag-Pol polyprotein3.4.23.160.458
4eh90OQMitogen-activated protein kinase 14/0.458
4j5j478Gag-Pol polyprotein3.4.23.160.458
1cm8ANPMitogen-activated protein kinase 12/0.457
1me8RVPInosine-5'-monophosphate dehydrogenase/0.457
1meiMOAInosine-5'-monophosphate dehydrogenase/0.457
1odyLP1Gag-Pol polyprotein3.4.23.160.457
2azzTCHPhospholipase A2, major isoenzyme3.1.1.40.457
2br1PFPSerine/threonine-protein kinase Chk12.7.11.10.457
3bxsDRSGag-Pol polyprotein3.4.23.160.457
3ddpRC8Cyclin-dependent kinase 22.7.11.220.457
3dndLL2cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.457
1k2c0Q4Gag-Pol polyprotein3.4.23.160.456
1pf9ADP60 kDa chaperonin/0.456
1unlRRCCyclin-dependent-like kinase 52.7.11.10.456
2b7zMK1Gag-Pol polyprotein/0.456
2qi5MZ7Gag-Pol polyprotein/0.456
3kddJZQGag-Pol polyprotein3.4.23.160.456
3nux3NVCyclin-dependent kinase 62.7.11.220.456
3nwq2NCGag-Pol polyprotein3.4.23.160.456
3upjU03Gag-Pol polyprotein/0.456
4js9H4BNitric oxide synthase, inducible1.14.13.390.456
4djhJDCKappa-type opioid receptor/0.456
2uy0HV1Gag-Pol polyprotein3.4.23.160.455
3nu5478Gag-Pol polyprotein3.4.23.160.455
3r71X86Cyclin-dependent kinase 22.7.11.220.455
1zthADPRIO-type serine/threonine-protein kinase Rio12.7.11.10.454
2q641UNGag-Pol polyprotein3.4.23.160.454
3rusADPChaperonin/0.454
3vfa031Gag-Pol polyprotein3.4.23.160.454
4dqc017Gag-Pol polyprotein/0.454
4eoi1ROCyclin-dependent kinase 22.7.11.220.454
4ft7H3KSerine/threonine-protein kinase Chk12.7.11.10.454
4hegG52Gag-Pol polyprotein3.4.23.160.454
5ks72BACarnitine transport ATP-binding protein OpuCA3.6.3.320.454
1b6pPI7Gag-Pol polyprotein3.4.23.160.453
1meuDMPGag-Pol polyprotein3.4.23.160.453
1s9jBBMDual specificity mitogen-activated protein kinase kinase 12.7.12.20.453
1sh9RITGag-Pol polyprotein3.4.23.160.453
1t7j478Gag-Pol polyprotein3.4.23.160.453
3dcrKVSProtease/0.453
4d4sBI9Focal adhesion kinase 12.7.10.20.453
4wbbADPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.453
1b6mPI6Gag-Pol polyprotein3.4.23.160.452
2bpv1INGag-Pol polyprotein3.4.23.160.452
3gubGUBDeath-associated protein kinase 12.7.11.10.452
3rm719ZCyclin-dependent kinase 22.7.11.220.452
3s00Z60Cyclin-dependent kinase 22.7.11.220.452
3sj7NDP3-oxoacyl-(Acyl-carrier-protein) reductase, putative/0.452
3ufnROCGag-Pol polyprotein/0.452
1d4yTPVGag-Pol polyprotein3.4.23.160.451
1qbsDMPGag-Pol polyprotein3.4.23.160.451
1ydtIQBcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.451
2f8g017Gag-Pol polyprotein3.4.23.160.451
2r5q1UNGag-Pol polyprotein/0.451
2uvzGVJcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.451
3d1xROCGag-Pol polyprotein3.4.23.160.451
3os33OSDual specificity mitogen-activated protein kinase kinase 12.7.12.20.451
4anqVGHALK tyrosine kinase receptor2.7.10.10.451
9hvp0E9Gag-Pol polyprotein/0.451
1qcfPP1Tyrosine-protein kinase HCK2.7.10.20.450
2c5nCK8Cyclin-dependent kinase 22.7.11.220.450
2ooyATP5'-AMP-activated protein kinase subunit gamma/0.450
2xk9XK9Serine/threonine-protein kinase Chk22.7.11.10.450
4h4uNDPBiphenyl dioxygenase ferredoxin reductase subunit/0.450
4iwxADPRibosomal protein S6--L-glutamate ligase/0.450
4s26SAHPhosphomethylpyrimidine synthase, chloroplastic4.1.99.170.450
4wlvNADMalate dehydrogenase, mitochondrial1.1.1.370.450
3qakUKAAdenosine receptor A2a/0.450
1c6x3INProtease/0.449
1hshMK1Gag-Pol polyprotein/0.449
1q8uH52cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
1sbgIM1Gag-Pol polyprotein/0.449
2c1bCQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
2pyn1UNGag-Pol polyprotein3.4.23.160.449
2uw7GVPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
4an92P7Dual specificity mitogen-activated protein kinase kinase 12.7.12.20.449
4bc6XZNSerine/threonine-protein kinase 102.7.11.10.449
4ftu7HKSerine/threonine-protein kinase Chk12.7.11.10.449
4q1x017Gag-Pol polyprotein3.4.23.160.449
6gsxGPSGlutathione S-transferase Mu 12.5.1.180.449
1d4kPI8Gag-Pol polyprotein3.4.23.160.448
1gx1CDP2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.448
1ke9LS5Cyclin-dependent kinase 22.7.11.220.448
2e9n76ASerine/threonine-protein kinase Chk12.7.11.10.448
2qd8065Gag-Pol polyprotein3.4.23.160.448
2uxzHI1Gag-Pol polyprotein3.4.23.160.448
2vo0M03cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
3aglA03cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.448
3c11GDMATP-dependent molecular chaperone HSP82/0.448
3juhANPCasein kinase II subunit alpha2.7.11.10.448
3mb714ICasein kinase II subunit alpha2.7.11.10.448
3v8w0G2Tyrosine-protein kinase ITK/TSK2.7.10.20.448
4ansVGHALK tyrosine kinase receptor2.7.10.10.448
4dqe017Gag-Pol polyprotein/0.448
4g170VNCasein kinase I isoform gamma-32.7.11.10.448
1c6zROCProtease/0.447
1ivq0PXGag-Pol polyprotein/0.447
1kzkJE2Gag-Pol polyprotein3.4.23.160.447
2brgDFYSerine/threonine-protein kinase Chk12.7.11.10.447
2ckeIQUDeath-associated protein kinase 2/0.447
3orn3ORDual specificity mitogen-activated protein kinase kinase 12.7.12.20.447
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
4an35Y0Dual specificity mitogen-activated protein kinase kinase 12.7.12.20.447
4i6aHMG3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.880.447
4jhz1KVBeta-glucuronidase3.2.1.310.447
4njt017Protease/0.447
1a9mU0EGag-Pol polyprotein/0.446
1hckATPCyclin-dependent kinase 22.7.11.220.446
1hiv1ZKGag-Pol polyprotein/0.446
1idb0DOGag-Pol polyprotein/0.446
1k6cMK1Gag-Pol polyprotein3.4.23.160.446
1rdwLARActin, alpha skeletal muscle/0.446
3i6oGR6Gag-Pol polyprotein3.4.23.160.446
3iro2CYBifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.446
3tkiS25Serine/threonine-protein kinase Chk12.7.11.10.446
3vs7KS1Tyrosine-protein kinase HCK2.7.10.20.446
4e5j581Polymerase acidic protein/0.446
4fk60UJTyrosine-protein kinase JAK1/0.446
4fsyHK7Serine/threonine-protein kinase Chk12.7.11.10.446
4gii0X6Non-receptor tyrosine-protein kinase TYK22.7.10.20.446
4z35ON9Lysophosphatidic acid receptor 1/0.446
3uzaT4GAdenosine receptor A2a/0.446
1ckpPVBCyclin-dependent kinase 22.7.11.220.445
1hpxKNIGag-Pol polyprotein/0.445
1msnJE2Gag-Pol polyprotein3.4.23.160.445
1q3sADPThermosome subunit alpha/0.445
2bpw1INGag-Pol polyprotein3.4.23.160.445
2qak1UNGag-Pol polyprotein3.4.23.160.445
2ycqUPXSerine/threonine-protein kinase Chk22.7.11.10.445
3q92XNBKetohexokinase/0.445
3rgaLSBEpoxide hydrolase LasB5.5.10.445
3s54017Protease/0.445
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
4riyADPEpidermal growth factor receptor2.7.10.10.445
4yuqKS1Calmodulin-like domain protein kinase/0.445
5aaaVGHALK tyrosine kinase receptor2.7.10.10.445
1npvL27Gag-Pol polyprotein3.4.23.160.444
2ayp43ASerine/threonine-protein kinase Chk12.7.11.10.444
2f7e2EAcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
2ijmADPFocal adhesion kinase 12.7.10.20.444
3ogqAB1Pol polyprotein/0.444
3qihFG7Gag-Pol polyprotein3.4.23.160.444
4axaRKDcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.444
4ehv0SJMitogen-activated protein kinase 14/0.444
4fkj11KCyclin-dependent kinase 22.7.11.220.444
4jseQJ2Nitric oxide synthase, brain1.14.13.390.444
4k110J9Proto-oncogene tyrosine-protein kinase Src2.7.10.20.444
1bvrTHTEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
1h1r6CPCyclin-dependent kinase 22.7.11.220.443
1h48CDI2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase4.6.1.120.443
1ke7LS3Cyclin-dependent kinase 22.7.11.220.443
1q3wATUGlycogen synthase kinase-3 beta2.7.11.260.443
1sduMK1Gag-Pol polyprotein3.4.23.160.443
2bb9AKCGag-Pol polyprotein3.4.23.160.443
2pwcG3GGag-Pol polyprotein3.4.23.160.443
2q54MU1Protease/0.443
3nls016Gag-Pol polyprotein3.4.23.160.443
3sayOFTGlycogen synthase kinase-3 beta2.7.11.260.443
3zo4QWIcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.443
4fg7ATPCalcium/calmodulin-dependent protein kinase type 12.7.11.170.443
4h0xNADIota toxin component Ia/0.443
4l455FIRibosomal protein S6 kinase beta-12.7.11.10.443
4trj665Enoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.443
1bygSTUTyrosine-protein kinase CSK/0.442
1hiiC20Gag-Pol polyprotein/0.442
1hnvTBOGag-Pol polyprotein2.7.7.490.442
1merDMQGag-Pol polyprotein3.4.23.160.442
1wbmBLLPol protein/0.442
2qi4MZ6Gag-Pol polyprotein/0.442
2vo3M04cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.442
2wmqZYQSerine/threonine-protein kinase Chk12.7.11.10.442
3el01UNGag-Pol polyprotein3.4.23.160.442
3gxoMQAMitomycin biosynthesis 6-O-methyltransferase/0.442
3oxv478Gag-Pol polyprotein3.4.23.160.442
3rf7NADIron-containing alcohol dehydrogenase/0.442
3vvh4BMDual specificity mitogen-activated protein kinase kinase 12.7.12.20.442
3w33W19Epidermal growth factor receptor2.7.10.10.442
4dce0JFALK tyrosine kinase receptor2.7.10.10.442
4ezj0SCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.442
4njsG08Protease/0.442
5aniES4Cyclin-dependent kinase 22.7.11.220.442
3ndtROCGag-Pol polyprotein3.4.23.160.441
4fsrHKCSerine/threonine-protein kinase Chk12.7.11.10.441
4lj7MNTChaperone protein ClpB/0.441
1bdqIM1Gag-Pol polyprotein3.4.23.160.440
1e8wQUEPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
1nf7RVPInosine-5'-monophosphate dehydrogenase 2/0.440
2b55D31Cyclin-dependent kinase 22.7.11.220.440
2b9fADPMitogen-activated protein kinase FUS32.7.11.240.440
2cn8DBQSerine/threonine-protein kinase Chk22.7.11.10.440
2j62GSZO-GlcNAcase NagJ/0.440
2j9mPY8Cyclin-dependent kinase 22.7.11.220.440
2qci065Gag-Pol polyprotein3.4.23.160.440
2qhyMZ1Gag-Pol polyprotein/0.440
2uzlC94Cyclin-dependent kinase 22.7.11.220.440
2yfxVGHALK tyrosine kinase receptor2.7.10.10.440
3bqr4RBDeath-associated protein kinase 3/0.440
3el4ROCGag-Pol polyprotein3.4.23.160.440
3pwrROCGag-Pol polyprotein3.4.23.160.440
4anv751Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4bcoT6QCyclin-dependent kinase 22.7.11.220.440
4fxfATPPyruvate kinase PKM2.7.1.400.440
5e8wSTUTGF-beta receptor type-12.7.11.300.440