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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
1ot3THMDeoxynucleoside kinase

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
1ot3THMDeoxynucleoside kinase/1.000
2vqsBVDDeoxynucleoside kinase/0.610
2jj8AZZDeoxynucleoside kinase/0.542
2gl0ADNUncharacterized protein/0.512
1bcpATPPertussis toxin subunit 4/0.507
1bcpATPPertussis toxin subunit 5/0.507
2rlcCHDCholoylglycine hydrolase3.5.1.240.493
1p72THMThymidine kinase/0.487
2v2zCDM4-diphosphocytidyl-2-C-methyl-D-erythritol kinase/0.485
1e2kTMCThymidine kinase/0.484
1qnfHDFDeoxyribodipyrimidine photo-lyase4.1.99.30.484
2nomDUTPoly(A) polymerase, putative/0.470
1t13INI6,7-dimethyl-8-ribityllumazine synthase 2/0.469
4dkjSAHCytosine-specific methyltransferase/0.469
2h447CAcGMP-specific 3',5'-cyclic phosphodiesterase/0.468
2mjiKTRFatty acid-binding protein, intestinal/0.468
4llkMEWcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.468
2b82ADNClass B acid phosphatase3.1.3.20.467
3ebiBEYM1 family aminopeptidase3.4.110.465
1xddAAYIntegrin alpha-L/0.464
3cr0809Wee1-like protein kinase2.7.10.20.464
4kfqKFQGlutamate receptor ionotropic, NMDA 1/0.464
3wqmB29Diterpene synthase3.1.7.80.463
4b144XBGlycylpeptide N-tetradecanoyltransferase/0.463
4fhf0TTSpore photoproduct lyase/0.463
1e2nRCAThymidine kinase/0.462
1sd1FMCS-methyl-5'-thioadenosine phosphorylase/0.462
4b13X25Glycylpeptide N-tetradecanoyltransferase/0.462
2cf8ESHProthrombin3.4.21.50.461
1stdBFSScytalone dehydratase4.2.1.940.460
1uhoVDNcGMP-specific 3',5'-cyclic phosphodiesterase/0.460
1x28PGUAspartate aminotransferase2.6.1.10.460
3qm4PN0Cytochrome P450 2D6/0.460
1zisINI6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.459
2w3aTOPDihydrofolate reductase1.5.1.30.459
4heu15JcAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.459
4j531J4Serine/threonine-protein kinase PLK12.7.11.210.459
3bx5304Mitogen-activated protein kinase 14/0.458
3i5xANPATP-dependent RNA helicase MSS116, mitochondrial3.6.4.130.458
3pdtADPMyosin heavy chain kinase A2.7.11.70.457
5jqhCAUBeta-2 adrenergic receptor/0.457
2gfsPQBMitogen-activated protein kinase 14/0.456
1dgfNDPCatalase1.11.1.60.455
2fm5M99cAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.455
3gyf51PDihydrofolate reductase1.5.1.30.455
3ndjJHZMethyltransferase/0.455
4l0oPLPCystathionine gamma-synthase2.5.1.480.455
1p6xTHMThymidine kinase/0.454
1ry0PG2Aldo-keto reductase family 1 member C3/0.454
2fjm073Tyrosine-protein phosphatase non-receptor type 13.1.3.480.454
3l05SN0N-acetylornithine carbamoyltransferase2.1.3.90.454
3q2jCKIAminoglycoside 3'-phosphotransferase2.7.1.950.454
4kp61S1cAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.454
4l5b1UXDeoxycytidine kinase2.7.1.740.454
1tilATPAnti-sigma F factor/0.453
3qi4IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.453
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.452
4b6s2HN3-dehydroquinate dehydratase4.2.1.100.452
4l321VFTankyrase-22.4.2.300.452
4b12C23Glycylpeptide N-tetradecanoyltransferase/0.451
1z5uCMPClass B acid phosphatase/0.450
3cfoGMPDNA-directed DNA polymerase/0.450
3l06SN0N-acetylornithine carbamoyltransferase2.1.3.90.450
3wd9QPCcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.450
4e0u0MVCyclic dipeptide N-prenyltransferase/0.450
2od7A1RNAD-dependent protein deacetylase HST23.5.10.449
2vp4DCPDeoxynucleoside kinase/0.449
3fowIMHPurine nucleoside phosphorylase/0.449
3g4kROLcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.449
3p0fBAUUridine phosphorylase 22.4.2.30.449
4kp71UQ1-deoxy-D-xylulose 5-phosphate reductoisomerase, apicoplastic1.1.1.2670.449
1zknIBMcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.448
3fpbATPSarcoplasmic/endoplasmic reticulum calcium ATPase 13.6.3.80.448
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
1nquRDL6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.447
1y2bDEEcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.447
2d32ANPGlutamate--cysteine ligase6.3.2.20.447
4a322CDGlycylpeptide N-tetradecanoyltransferase/0.447
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.447
4zzjCNANAD-dependent protein deacetylase sirtuin-13.5.10.447
1w19T1P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.446
2v7qADPATP synthase subunit beta, mitochondrial3.6.3.140.446
2w3mFOLDihydrofolate reductase1.5.1.30.446
2y60M8FIsopenicillin N synthase1.21.3.10.446
4a83DXCMajor pollen allergen Bet v 1-A/0.446
1c4yIH3Prothrombin3.4.21.50.445
1e66HUXAcetylcholinesterase3.1.1.70.445
3bi6396Wee1-like protein kinase2.7.10.20.445
3dz7O8MS-adenosylmethionine decarboxylase proenzyme4.1.1.500.445
3hy9098A disintegrin and metalloproteinase with thrombospondin motifs 53.4.240.445
3uyk0CXProbable NDP-rhamnosyltransferase/0.445
3w5eNVWcAMP-specific 3',5'-cyclic phosphodiesterase 4B3.1.4.530.445
5aglH4BNitric oxide synthase, brain1.14.13.390.445
1kr3113Metallo-beta-lactamase type 2/0.444
1w19T4P6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.444
2cf9348Prothrombin3.4.21.50.444
2ivnANPtRNA N6-adenosine threonylcarbamoyltransferase/0.444
2vqqTFGHistone deacetylase 43.5.1.980.444
3c36KAIGlutamate receptor ionotropic, kainate 1/0.444
3e92G6AMitogen-activated protein kinase 14/0.444
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3vo2FADFerredoxin--NADP reductase/0.444
1kmsLIHDihydrofolate reductase1.5.1.30.443
3wv9FEGHmd co-occurring protein HcgE/0.443
4fhd0TTSpore photoproduct lyase/0.443
4yaw2AMNADPH--cytochrome P450 reductase/0.443
2oliIOPBasic phospholipase A2 VRV-PL-VIIIa3.1.1.40.442
3rgaILDEpoxide hydrolase LasB5.5.10.442
3tvqDQHMultifunctional cyclase-dehydratase-3-O-methyl transferase TcmN2.1.10.442
4a30QMIGlycylpeptide N-tetradecanoyltransferase/0.442
4ajfF03cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A3.1.4.170.442
4ctjSAMGenome polyprotein/0.442
4pnmNU1Tankyrase-22.4.2.300.442
4wo5324Serine/threonine-protein kinase B-raf2.7.11.10.442
1e2jTHMThymidine kinase/0.441
1mkdZARcAMP-specific 3',5'-cyclic phosphodiesterase 4D3.1.4.530.441
1yw9A84Methionine aminopeptidase 2/0.441
2bgsNDPAldose reductase1.1.1.210.441
2c94TSF6,7-dimethyl-8-ribityllumazine synthase2.5.1.780.441
2o6hINI6,7-dimethyl-8-ribityllumazine synthase 12.5.1.780.441
2zi63D1Deoxycytidine kinase2.7.1.740.441
3dy85GPHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
4jln18VDeoxycytidine kinase2.7.1.740.441
4kq6DLZ6,7-dimethyl-8-ribityllumazine synthase/0.441
1gpuTHDTransketolase 12.2.1.10.440
1pqc444Oxysterols receptor LXR-beta/0.440
1yciNDFHypoxia-inducible factor 1-alpha inhibitor1.14.11.300.440
1zdgUPGGlycogenin-12.4.1.1860.440
2bu9HFVIsopenicillin N synthase1.21.3.10.440
2pauD5M5'-deoxynucleotidase YfbR/0.440
2wgs1AZGlutamine synthetase6.3.1.20.440
3gueUPGUTP-glucose-1-phosphate uridylyltransferase 2, putative/0.440
3mauEXTPutative sphingosine-1-phosphate lyase/0.440
4a81DXCMajor pollen allergen Bet v 1-A/0.440
4li61XOTankyrase-12.4.2.300.440