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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Binding site similarity measured by Shaper
You can zoom onto the graph by using the mouse to make a selection

Binding Sites 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
Binding Sites are considered as similar when the similarity value is greater than 0.44

Reference Protein Data Bank Entry :
PDB IDHETUniprot NameEC Number
3lutNAPVoltage-gated potassium channel subunit beta-2

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
3lutNAPVoltage-gated potassium channel subunit beta-2/1.000
1qrqNDPVoltage-gated potassium channel subunit beta-2/0.530
4jtcNAPVoltage-gated potassium channel subunit beta-2/0.519
4itxIN5Cystathionine beta-lyase MetC4.4.1.80.487
2gmuPDGPutative pyridoxamine 5-phosphate-dependent dehydrase/0.482
3b8xG4MPutative pyridoxamine 5-phosphate-dependent dehydrase/0.482
4to6TTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.482
1a8rGTPGTP cyclohydrolase 13.5.4.160.480
1nlmUD1UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol N-acetylglucosamine transferase/0.480
4to4DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.479
1gveNAPAflatoxin B1 aldehyde reductase member 310.476
4to1DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.476
4j7gTRHPCZA361.3/0.475
4j7hTRHPCZA361.3/0.472
4bfyZVYPantothenate kinase2.7.1.330.471
2gevCOKPantothenate kinase2.7.1.330.470
2cf9348Prothrombin3.4.21.50.469
4kq2U5PGlycogen [starch] synthase isoform 22.4.1.110.469
1rvvINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.467
4e2yJHZMethyltransferase/0.467
3jusBCDLanosterol 14-alpha demethylase1.14.13.700.466
4kbyC2EStimulator of interferon genes protein/0.466
4k97ATPCyclic GMP-AMP synthase/0.464
4rxrDCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.464
3bl7DD1m7GpppX diphosphatase3.6.1.590.463
4kfqKFQGlutamate receptor ionotropic, NMDA 1/0.463
1kyvRBF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.462
2q85973UDP-N-acetylenolpyruvoylglucosamine reductase1.3.1.980.462
3hggCHDCmeR/0.462
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.462
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.459
4qg0DUTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.459
1eyyNAPNADP-dependent fatty aldehyde dehydrogenase1.2.1.40.458
3uzwNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.458
1nqvLMZ6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.456
2cf8ESHProthrombin3.4.21.50.455
2xlpNAPPutative flavin-containing monooxygenase/0.455
1kyxCRM6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.454
4ayy9MXProthrombin3.4.21.50.454
4tnzTTPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.454
1oxoIK2Aspartate aminotransferase, mitochondrial2.6.1.10.453
4gv4MEJPoly [ADP-ribose] polymerase 32.4.2.300.453
1obnASVIsopenicillin N synthase1.21.3.10.452
3dr4G4MGDP-perosamine synthase/0.452
3nljH4BNitric oxide synthase, brain1.14.13.390.451
3qiyQI1Botulinum neurotoxin type A3.4.24.690.451
3rsv3RSBeta-secretase 13.4.23.460.451
5dp2NAPCurF/0.451
2x90EALAngiotensin-converting enzyme3.4.15.10.450
4rxqDUTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.450
4rn615UProthrombin3.4.21.50.449
2a2dANPN-acetylgalactosamine kinase2.7.1.1570.448
3dr7GPDGDP-perosamine synthase/0.448
3kr6UD1UDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.448
3qkzNAPAldose reductase-related protein 11.1.1.210.448
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.448
2gesCOKPantothenate kinase2.7.1.330.447
2gmsP0PPutative pyridoxamine 5-phosphate-dependent dehydrase/0.447
3c4hDRLPoly [ADP-ribose] polymerase 32.4.2.300.447
3qdlFMNOxygen-insensitive NADPH nitroreductase/0.447
4h0vNADIota toxin component Ia/0.447
4kxjP34Nucleoprotein/0.447
1qs2NADVip2Ac/0.446
1rt9IMHPurine nucleoside phosphorylase2.4.2.10.446
1x1cSAHC-20 methyltransferase/0.446
2zryFNRIsopentenyl-diphosphate delta-isomerase/0.446
3i12ADPD-alanine--D-alanine ligase A6.3.2.40.446
4b68NAPL-ornithine N(5)-monooxygenase/0.446
4fl0PLPAminotransferase ALD1, chloroplastic2.6.10.446
4lez1SYCyclic GMP-AMP synthase/0.446
4to0DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.446
4to3DCPDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.446
1wuaAP8Actin, alpha skeletal muscle/0.445
2po3T4K4-dehydrase/0.445
2x91LPRAngiotensin-converting enzyme3.4.15.10.445
4arbC57Acetylcholinesterase3.1.1.70.445
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.445
4mlp2CXCryptochrome-2/0.445
1lnmDTXBilin-binding protein/0.444
1qtiGNTAcetylcholinesterase3.1.1.70.444
2e94364Geranylgeranyl pyrophosphate synthase/0.444
2hp2KE4Glutamate-1-semialdehyde 2,1-aminomutase5.4.3.80.444
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
1fyfSSAThreonine--tRNA ligase6.1.1.30.443
1ypkCCRProthrombin3.4.21.50.443
1umaIN2Prothrombin3.4.21.50.442
1ypjUIBProthrombin3.4.21.50.442
1yzqGNPRas-related protein Rab-6A/0.442
2cn0F25Prothrombin3.4.21.50.442
2e8uIPEGeranylgeranyl pyrophosphate synthase/0.442
2fq6P3FCystathionine beta-lyase MetC4.4.1.80.442
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.442
3e6eDCSAlanine racemase/0.442
4b2gV1NUncharacterized protein/0.442
1a9cGTPGTP cyclohydrolase 13.5.4.160.441
1nqw5YL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
2v3oI26Prothrombin3.4.21.50.441
2yvwEPUUDP-N-acetylglucosamine 1-carboxyvinyltransferase/0.441
3buvNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.441
3hl0NADMaleylacetate reductase/0.441
4ko8AGSTransitional endoplasmic reticulum ATPase3.6.4.60.441
1bk0ACVIsopenicillin N synthase1.21.3.10.440
1t3zCAOFormyl-CoA:oxalate CoA-transferase/0.440
2bvs2CEProthrombin3.4.21.50.440
2c6c24IGlutamate carboxypeptidase 23.4.17.210.440
3frkTQPQdtB/0.440
3sqzCOAPutative hydroxymethylglutaryl-CoA synthase/0.440
3uoxFAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase1.14.13.1600.440
4gh6LUOHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.440
4tnyDGTDeoxynucleoside triphosphate triphosphohydrolase SAMHD13.1.50.440