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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
2c96ATPPsp operon transcriptional activator

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
2c96ATPPsp operon transcriptional activator/1.000
4qosADPPsp operon transcriptional activator/0.585
2c9cATPPsp operon transcriptional activator/0.533
3dzdADPTranscriptional regulator (NtrC family)/0.521
1ny5ADPTranscriptional regulator (NtrC family)/0.515
3m0eATPTranscriptional regulator (NtrC family)/0.512
3qtsX46Cyclin-dependent kinase 22.7.11.220.481
2chz093Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.480
1e8xATPPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.476
1ykdCMPAdenylate cyclase/0.476
3cd57HI3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.473
3zvvXAZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.472
4j6i1JVPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.471
3vsoEK1Peroxisome proliferator-activated receptor gamma/0.470
4ezj0SCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.470
3rpr25ZCyclin-dependent kinase 22.7.11.220.469
4ezk0SDPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.469
3ls8AJZPhosphatidylinositol 3-kinase catalytic subunit type 32.7.1.1370.467
2a5uQYTPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.464
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.464
1ht2ADPATP-dependent protease ATPase subunit HslU/0.463
3lj3WYEPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.463
4anv751Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.463
1e8zSTUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.462
4iirANPSerine/threonine-protein kinase PRP4 homolog2.7.11.10.462
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.461
1e7vLY2Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.460
3ibqATPPyridoxal kinase/0.460
4fhk0U0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.460
4l23X6KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform/0.460
4o0rX4ZSerine/threonine-protein kinase PAK 12.7.11.10.459
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.458
3lamKRPGag-Pol polyprotein2.7.7.490.458
4ezl0SEPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.458
2ze2T27Gag-Pol polyprotein2.7.7.490.457
2zb0GK3Mitogen-activated protein kinase 14/0.456
4wujFMNGlycoside hydrolase family 15, cellulose signaling associated protein envoy/0.456
2i4zDRHPeroxisome proliferator-activated receptor gamma/0.455
3qk0QK0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.455
4dit0KDGlycogen synthase kinase-3 beta2.7.11.260.455
2b9wFADPutative aminooxidase/0.454
3gbuATPUncharacterized sugar kinase PH14592.7.10.454
3njoP2MAbscisic acid receptor PYR1/0.454
1rdt570Peroxisome proliferator-activated receptor gamma/0.453
3lfcZ86Mitogen-activated protein kinase 14/0.453
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
3nnxEDDMitogen-activated protein kinase 14/0.453
3s2a2NQPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.453
1g6cIFPThiamine-phosphate synthase/0.452
2c6dANPAurora kinase A2.7.11.10.452
3gcuR48Mitogen-activated protein kinase 14/0.452
3l08ZIGPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
3p5kP5KMitogen-activated protein kinase 14/0.452
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
4mxxDB8Proto-oncogene tyrosine-protein kinase Src2.7.10.20.452
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.451
3ig7EFPCyclin-dependent kinase 22.7.11.220.451
3r9nZ68Cyclin-dependent kinase 22.7.11.220.451
4bqpNADEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.451
4gb90WRPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.451
4gk4L90Ephrin type-A receptor 32.7.10.10.451
4r1lADPPhenylacetate-coenzyme A ligase/0.451
1ikwEFZGag-Pol polyprotein2.7.7.490.450
1s0zEB1Vitamin D3 receptor/0.450
2p4yC03Peroxisome proliferator-activated receptor gamma/0.450
3d0bSNXHeat shock protein HSP 90-alpha/0.450
4fuyEK2Mitogen-activated protein kinase 12.7.11.240.450
4hys1BJMitogen-activated protein kinase 82.7.11.240.450
4jy2FAD2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase/0.450
5iqeGNPBifunctional AAC/APH2.3.10.450
1e79ADPATP synthase subunit alpha, mitochondrial/0.449
1e79ADPATP synthase subunit beta, mitochondrial3.6.3.140.449
1mruAGSSerine/threonine-protein kinase PknB2.7.11.10.449
1q97ATPSerine/threonine-protein kinase SKY12.7.11.10.449
1uykPUXHeat shock protein HSP 90-alpha/0.449
2yfeYFEPeroxisome proliferator-activated receptor gamma/0.449
3au8NDP1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.449
3rk909ZCyclin-dependent kinase 22.7.11.220.449
3uli1N3Cyclin-dependent kinase 22.7.11.220.449
4hee14RPeroxisome proliferator-activated receptor gamma/0.449
4jlcSU6Serine/threonine-protein kinase TBK12.7.11.10.449
3hyoADPPyridoxal kinase/0.448
3k3jF4CMitogen-activated protein kinase 14/0.448
4hvb19PPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
4mq22C4Dual specificity tyrosine-phosphorylation-regulated kinase 1A2.7.12.10.448
1s4mLUMRiboflavin biosynthesis protein/0.447
2v4lABJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
2zzaFOLDihydrofolate reductase/0.447
4hyu1BKMitogen-activated protein kinase 82.7.11.240.447
4xe606UDihydrofolate reductase1.5.1.30.447
4yduADPtRNA N6-adenosine threonylcarbamoyltransferase/0.447
1uyhPU0Heat shock protein HSP 90-alpha/0.446
2b0m201Dihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.446
3n8zFLPProstaglandin G/H synthase 11.14.99.10.446
4jlm1NNDeoxycytidine kinase2.7.1.740.446
1im2ADPATP-dependent protease ATPase subunit HslU/0.445
2r5tANPSerine/threonine-protein kinase Sgk12.7.11.10.445
3a60STURibosomal protein S6 kinase beta-12.7.11.10.445
3ds6A17Mitogen-activated protein kinase 14/0.445
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
4crsAGSSerine/threonine-protein kinase N22.7.11.130.445
4dk50KOPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
4i2q1BTGag-Pol polyprotein2.7.7.490.445
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.445
4xf7ACPCarbohydrate/pyrimidine kinase, PfkB family/0.445
5djuFMNNPH1-2/0.445
1jpaANPEphrin type-B receptor 22.7.10.10.444
1zeoC01Peroxisome proliferator-activated receptor gamma/0.444
2i4jDRJPeroxisome proliferator-activated receptor gamma/0.444
2phkATPPhosphorylase b kinase gamma catalytic chain, skeletal muscle/heart isoform2.7.11.190.444
3b8r887Vascular endothelial growth factor receptor 22.7.10.10.444
3r8vZ62Cyclin-dependent kinase 22.7.11.220.444
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4bwxAGSPAB-dependent poly(A)-specific ribonuclease subunit pan3/0.444
4h9814QUncharacterized protein/0.444
1e90MYCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
3rinI2OMitogen-activated protein kinase 14/0.443
3uibSB2Putative mitogen-activated protein kinase/0.443
4flh14KPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4ft3H1KSerine/threonine-protein kinase Chk12.7.11.10.443
4oauADP2-5A-dependent ribonuclease3.1.260.443
2i51FMNPyridoxamine 5'-phosphate oxidase-related, FMN-binding/0.442
2yn8STUEphrin type-B receptor 42.7.10.10.442
3qlhT27Gag-Pol polyprotein2.7.7.490.442
4em9TCEPeroxisome proliferator-activated receptor gamma/0.442
4fhj0TZPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4gmy0X5Tyrosine-protein kinase JAK2/0.442
4o1pANPRibonuclease L/0.442
1e94ANPATP-dependent protease ATPase subunit HslU/0.441
1rt5UC2Gag-Pol polyprotein2.7.7.490.441
1unhIXMCyclin-dependent-like kinase 52.7.11.10.441
2i4pDRHPeroxisome proliferator-activated receptor gamma/0.441
3dpd41APhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
3srqQ19Dihydrofolate reductase1.5.1.30.441
3uvp048Mitogen-activated protein kinase 14/0.441
4achKDIGlycogen synthase kinase-3 beta2.7.11.260.441
4fgg0U5Dihydrofolate reductase1.5.1.30.441
4otpADPSerine/threonine-protein kinase RIO12.7.11.10.441
1qxlFR8Adenosine deaminase3.5.4.40.440
2j0vGDPRac-like GTP-binding protein ARAC7/0.440
2qoqANPEphrin type-A receptor 32.7.10.10.440
3flsFLSMitogen-activated protein kinase 14/0.440
3ml9ML9Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
3r8uZ31Cyclin-dependent kinase 22.7.11.220.440
4bi1ZO6Dual specificity protein kinase TTK2.7.12.10.440
4orkGDPBifunctional AAC/APH2.3.10.440