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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
1z59ADPType 2 DNA topoisomerase 6 subunit B

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
1z59ADPType 2 DNA topoisomerase 6 subunit B/1.000
3t10ACPHeat shock protein HSP 90-alpha/0.586
4xcjADPHeat shock cognate 90 kDa protein/0.576
3t2sAGSHeat shock protein HSP 90-alpha/0.568
1byqADPHeat shock protein HSP 90-alpha/0.566
4gqtADPHeat shock protein 90/0.559
2yefANPHeat shock protein HSP 90-alpha/0.558
5f5rANPHeat shock protein 75 kDa, mitochondrial/0.550
2e0aANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.549
2xk2ADPHeat shock protein HSP 90-alpha/0.547
4jqlVJ6Heat shock protein HSP 90-alpha/0.545
1yt0ADPEndoplasmin/0.544
3r4oFU3Heat shock protein HSP 90-alpha/0.540
2hkjRDCType 2 DNA topoisomerase 6 subunit B/0.539
1y4sADPChaperone protein HtpG/0.532
1qy5NECEndoplasmin/0.530
3iedAN2HSP90/0.530
4xclAGSHeat shock cognate 90 kDa protein/0.530
2xhrC0PHeat shock protein HSP 90-alpha/0.529
3crlANP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial2.7.11.20.529
1am1ADPATP-dependent molecular chaperone HSP82/0.527
2bu8ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial2.7.11.20.527
4egkRDCHeat shock protein HSP 90-alpha/0.522
1amwADPATP-dependent molecular chaperone HSP82/0.521
3k99PFTHeat shock protein HSP 90-alpha/0.519
3d2rADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.516
3t1kANPHeat shock protein HSP 90-alpha/0.515
1uy7PU4Heat shock protein HSP 90-alpha/0.513
2bt0CT5Heat shock protein HSP 90-alpha/0.510
2qg0A94Heat shock protein HSP 90-alpha/0.510
3h4lANPDNA mismatch repair protein PMS1/0.510
4bqjXKLHeat shock protein HSP 90-alpha/0.510
1u0zRDCEndoplasmin/0.508
3hhu819Heat shock protein HSP 90-alpha/0.507
2xabVHDHeat shock protein HSP 90-alpha/0.506
2xhtC0YHeat shock protein HSP 90-alpha/0.506
1bgqRDCATP-dependent molecular chaperone HSP82/0.505
3hyz42CHeat shock protein HSP 90-alpha/0.504
1h7uAGSMismatch repair endonuclease PMS23.10.503
2yee2ECHeat shock protein HSP 90-alpha/0.500
3r4pFU7Heat shock protein HSP 90-alpha/0.500
4ce2BO5ATP-dependent molecular chaperone HSP82/0.499
2iwuNP5ATP-dependent molecular chaperone HSP82/0.497
2xd6XD6ATP-dependent molecular chaperone HSP82/0.496
2ykiYKIHeat shock protein HSP 90-alpha/0.496
2zkjADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.496
1i5aACPChemotaxis protein CheA2.7.13.30.495
2bu2ATP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial2.7.11.20.495
2wi6ZZ6Heat shock protein HSP 90-alpha/0.495
2xcmADPCytosolic heat shock protein 90/0.495
3o0iP54Heat shock protein HSP 90-alpha/0.495
1uy9PU6Heat shock protein HSP 90-alpha/0.494
2werRDCATP-dependent molecular chaperone HSP82/0.494
4egiB2JHeat shock protein HSP 90-alpha/0.494
3t0zATPHeat shock protein HSP 90-alpha/0.493
2iwxM1SATP-dependent molecular chaperone HSP82/0.492
2xx213CATP-dependent molecular chaperone HSP82/0.492
1uy8PU5Heat shock protein HSP 90-alpha/0.491
1uyiPUZHeat shock protein HSP 90-alpha/0.491
1z5cADPType 2 DNA topoisomerase 6 subunit B/0.491
2wepADPATP-dependent molecular chaperone HSP82/0.490
1yc443PHeat shock protein HSP 90-alpha/0.488
2byh2D7Heat shock protein HSP 90-alpha/0.488
2zdyADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.488
3ekoPYUHeat shock protein HSP 90-alpha/0.488
3ekrPY9Heat shock protein HSP 90-alpha/0.488
3hz142CHeat shock protein HSP 90-alpha/0.488
2yegXQGHeat shock protein HSP 90-alpha/0.487
1gjvAGS[3-methyl-2-oxobutanoate dehydrogenase [lipoamide]] kinase, mitochondrial2.7.11.40.486
2gfdRDAEndoplasmin/0.486
2qg2A91Heat shock protein HSP 90-alpha/0.485
2xx413IATP-dependent molecular chaperone HSP82/0.485
1nhhANPDNA mismatch repair protein MutL/0.484
2ykbYKBHeat shock protein HSP 90-alpha/0.484
2yxuATPPyridoxal kinase2.7.1.350.484
2zdxP4A[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 4, mitochondrial2.7.11.20.484
2yeiXQIHeat shock protein HSP 90-alpha/0.483
4as94QSATP-dependent molecular chaperone HSP82/0.483
4hy6FJ1Heat shock protein HSP 90-alpha/0.482
1u0yPA7Endoplasmin/0.480
2ykjYKJHeat shock protein HSP 90-alpha/0.480
4egh0OYHeat shock protein HSP 90-alpha/0.480
1i5bANPChemotaxis protein CheA2.7.13.30.479
3q5kD1UHeat shock protein 83-1/0.479
1uykPUXHeat shock protein HSP 90-alpha/0.478
1zxnADPDNA topoisomerase 2-alpha5.99.1.30.478
2o1uANPEndoplasmin/0.477
3whaWHAHeat shock protein HSP 90-alpha/0.477
4ce17FKATP-dependent molecular chaperone HSP82/0.476
2gqpPA7Endoplasmin/0.475
2qfoA13Heat shock protein HSP 90-alpha/0.475
2yjxYJXHeat shock protein HSP 90-alpha/0.475
2fxsRDAATP-dependent molecular chaperone HSP82/0.474
1i59ANPChemotaxis protein CheA2.7.13.30.473
1qy8RDIEndoplasmin/0.472
3a0tADPSensor histidine kinase/0.472
3r4nFU5Heat shock protein HSP 90-alpha/0.472
3rlr3RRHeat shock protein HSP 90-alpha/0.472
1i58ACPChemotaxis protein CheA2.7.13.30.469
2briANPUridylate kinase2.7.4.220.469
3b28B2XHeat shock protein HSP 90-alpha/0.469
2breKJ2ATP-dependent molecular chaperone HSP82/0.468
4eftEFTHeat shock protein HSP 90-alpha/0.468
2fypRDEEndoplasmin/0.467
4asf62UATP-dependent molecular chaperone HSP82/0.467
3zw3ZW3Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.466
4fl2ANPTyrosine-protein kinase SYK2.7.10.20.466
1mx0ANPType 2 DNA topoisomerase 6 subunit B/0.465
2vcj2EQHeat shock protein HSP 90-alpha/0.465
1i59ADPChemotaxis protein CheA2.7.13.30.464
2wi72KLHeat shock protein HSP 90-alpha/0.463
1yszNECEndoplasmin/0.462
3pehIBDEndoplasmin homolog, putative/0.462
2brcCT5ATP-dependent molecular chaperone HSP82/0.461
4xc0ACPHeat shock cognate 90 kDa protein/0.461
3rlq3RQHeat shock protein HSP 90-alpha/0.460
4a99FADTetX family tetracycline inactivation enzyme/0.460
4anx534Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.459
2o1vADPEndoplasmin/0.458
4awq592Heat shock protein HSP 90-alpha/0.458
2xx513NATP-dependent molecular chaperone HSP82/0.457
3v1yNADGlyceraldehyde-3-phosphate dehydrogenase 1, cytosolic1.2.1.120.457
4fcr0TMHeat shock protein HSP 90-alpha/0.457
1nzdUPGDNA beta-glucosyltransferase/0.456
3tm0ANPAminoglycoside 3'-phosphotransferase2.7.1.950.456
1yc34BCHeat shock protein HSP 90-alpha/0.455
2q8iRDC[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrial2.7.11.20.455
2yi5YI5Heat shock protein HSP 90-alpha/0.455
4ii5ADPCyclin-dependent kinase 22.7.11.220.455
4r3aANPBlue-light-activated histidine kinase 22.7.13.30.455
1zthADPRIO-type serine/threonine-protein kinase Rio12.7.11.10.454
3ft5MO8Heat shock protein HSP 90-alpha/0.454
4gyiADPUncharacterized protein/0.454
4lb2DM5Serum albumin/0.454
4lrjANPUncharacterized protein/0.454
3nszANPCasein kinase II subunit alpha2.7.11.10.453
4asg814ATP-dependent molecular chaperone HSP82/0.453
3sl2ATPSensor histidine kinase WalK/0.452
4ce3L4VATP-dependent molecular chaperone HSP82/0.452
4hj3FMNLOV protein/0.452
1jm6ADP[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 2, mitochondrial2.7.11.20.451
2xs0ANPMitogen-activated protein kinase 82.7.11.240.451
4y9qC2EUncharacterized protein/0.451
2cjmATPCyclin-dependent kinase 22.7.11.220.450
2excJNKMitogen-activated protein kinase 102.7.11.240.450
2f4bEHAPeroxisome proliferator-activated receptor gamma/0.450
2ykcYKCHeat shock protein HSP 90-alpha/0.450
4k28NADShikimate dehydrogenase family protein/0.450
2l1rSXKTroponin C, slow skeletal and cardiac muscles/0.449
2qfoA51Heat shock protein HSP 90-alpha/0.449
3c11GDMATP-dependent molecular chaperone HSP82/0.449
3otwCOAPhosphopantetheine adenylyltransferase/0.449
1uzwCDHIsopenicillin N synthase1.21.3.10.448
2tmdADPTrimethylamine dehydrogenase1.5.8.20.447
2y3rTRKTamL/0.447
1nzfUPGDNA beta-glucosyltransferase/0.446
1x8vESLLanosterol 14-alpha demethylase1.14.13.700.446
2hog710Serine/threonine-protein kinase Chk12.7.11.10.446
5dpvSKEAurora kinase A2.7.11.10.446
3hekBD0Heat shock protein HSP 90-alpha/0.445
4hjfC2EGGDEF family protein/0.445
4ijrNDPD-arabinose dehydrogenase [NAD(P)+] heavy chain1.1.1.1170.445
1j1cADPGlycogen synthase kinase-3 beta2.7.11.260.444
3fr4F8AFatty acid-binding protein, adipocyte/0.444
4awp99AHeat shock protein HSP 90-alpha/0.444
1qrrUPGUDP-sulfoquinovose synthase, chloroplastic3.13.1.10.443
1in5ADPHolliday junction ATP-dependent DNA helicase RuvB/0.442
4du82P0Mevalonate diphosphate decarboxylase/0.442
4ix5ANPUncharacterized protein/0.442
4y12AGSSerine/threonine-protein kinase PknG2.7.11.10.442
5c7oNADGlyceraldehyde-3-phosphate dehydrogenase, testis-specific1.2.1.120.442
2q46NAPUncharacterized protein At5g02240/0.441
3el9DR7Gag-Pol polyprotein3.4.23.160.441
3swrSFGDNA (cytosine-5)-methyltransferase 12.1.1.370.441
4f081RSTyrosine-protein kinase JAK2/0.441
1tqf32PBeta-secretase 13.4.23.460.440
1u8fNADGlyceraldehyde-3-phosphate dehydrogenase1.2.1.120.440
1uycPU7Heat shock protein HSP 90-alpha/0.440
2bz5AB4Heat shock protein HSP 90-alpha/0.440
2ddoATPPyridoxine/pyridoxal/pyridoxamine kinase/0.440
2qenADPWalker-Type ATPase/0.440
4a6nFADTetX family tetracycline inactivation enzyme/0.440
4wucANPDNA gyrase subunit B/0.440