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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
2dfdNADMalate dehydrogenase, mitochondrial1.1.1.37

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
2dfdNADMalate dehydrogenase, mitochondrial1.1.1.371.000
4wluNADMalate dehydrogenase, mitochondrial1.1.1.370.602
3zk5Z18Cytochrome P450 monooxygenase PikC/0.529
4b7sQLECytochrome P450 monooxygenase PikC/0.505
5dqrFAD7-hydroxymethyl chlorophyll a reductase, chloroplastic1.17.7.20.490
4b7dQLECytochrome P450 monooxygenase PikC/0.489
1jioDEB6-deoxyerythronolide B hydroxylase/0.486
2c6hPXICytochrome P450 monooxygenase PikC/0.486
1i7iAZ2Peroxisome proliferator-activated receptor gamma/0.485
2ath3EAPeroxisome proliferator-activated receptor gamma/0.478
3cs8BRLPeroxisome proliferator-activated receptor gamma/0.478
3p3zP3ZPutative cytochrome P450/0.477
2cmwOLPCasein kinase I isoform gamma-12.7.11.10.475
2ca0PXICytochrome P450 monooxygenase PikC/0.474
4aw3MYVMycinamicin IV hydroxylase/epoxidase/0.472
4k1b1OCSerine/threonine-protein kinase pim-12.7.11.10.472
4z69DIFSerum albumin/0.472
3fhyATPPyridoxal kinase2.7.1.350.471
3orzBI43-phosphoinositide-dependent protein kinase 12.7.11.10.471
2c7xNRBCytochrome P450 monooxygenase PikC/0.470
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.470
2ckeIQUDeath-associated protein kinase 2/0.469
2y8qADP5'-AMP-activated protein kinase subunit gamma-1/0.469
3qaiXNNKetohexokinase/0.469
4cy8FDA2-hydroxybiphenyl-3-monooxygenase/0.469
3e8nVRADual specificity mitogen-activated protein kinase kinase 12.7.12.20.468
4biiPYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.468
3a99ANPSerine/threonine-protein kinase pim-12.7.11.10.467
1qpjSTUTyrosine-protein kinase Lck2.7.10.20.466
1tqpATPRIO-type serine/threonine-protein kinase Rio22.7.11.10.466
3w0sANPHygromycin-B 4-O-kinase2.7.1.1630.465
5eypLOCTubulin beta chain/0.464
1mabATPATP synthase subunit alpha, mitochondrial/0.463
1zarADPRIO-type serine/threonine-protein kinase Rio22.7.11.10.463
1gufNDPEnoyl-[acyl-carrier-protein] reductase 1, mitochondrial1.3.1.100.462
3c0i3AMPeripheral plasma membrane protein CASK2.7.11.10.462
3qk0QK0Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.462
4gmy0X5Tyrosine-protein kinase JAK2/0.462
4izy1J2Mitogen-activated protein kinase 82.7.11.240.462
1k6pXN3Gag-Pol polyprotein3.4.23.160.461
1pmn984Mitogen-activated protein kinase 102.7.11.240.460
2vzmNRBCytochrome P450 monooxygenase PikC/0.460
4enhFVXCholesterol 24-hydroxylase/0.460
4jvf17XRetinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta/0.459
1t1rIMB1-deoxy-D-xylulose 5-phosphate reductoisomerase1.1.1.2670.458
1tqmANPRIO-type serine/threonine-protein kinase Rio22.7.11.10.458
1uu7BI23-phosphoinositide-dependent protein kinase 12.7.11.10.458
3eek53SUncharacterized protein/0.458
4c58824Cyclin-G-associated kinase2.7.11.10.458
5itzLOCTubulin beta-2B chain/0.458
1s9jBBMDual specificity mitogen-activated protein kinase kinase 12.7.12.20.457
1zaoATPRIO-type serine/threonine-protein kinase Rio22.7.11.10.457
2wtdZZKSerine/threonine-protein kinase Chk22.7.11.10.457
4enyJ19Serine/threonine-protein kinase pim-12.7.11.10.457
4l4cCAMCamphor 5-monooxygenase1.14.15.10.457
4lrzADPPEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL2.70.457
2bxiAZQSerum albumin/0.456
2qhcAB1Protease/0.456
2vxoXMPGMP synthase [glutamine-hydrolyzing]6.3.5.20.456
2bmcMPYAurora kinase A2.7.11.10.455
3cktYDPGag-Pol polyprotein3.4.23.160.455
4enxZ20Serine/threonine-protein kinase pim-12.7.11.10.455
5cvfATPCasein kinase II subunit alpha2.7.11.10.455
1e7vLY2Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
1o8cNDPProbable acrylyl-CoA reductase AcuI1.3.1.840.454
2xckMH43-phosphoinositide-dependent protein kinase 12.7.11.10.454
2y1oT26UDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.454
3opdHIEHeat shock protein 83/0.454
3p2eSAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.454
3pt6SAHDNA (cytosine-5)-methyltransferase 12.1.1.370.454
4bgiI4IEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.454
4tuvCPZCytochrome P450 1191.140.454
1uuoBRFDihydroorotate dehydrogenase (quinone), mitochondrial1.3.5.20.453
2exlGDMEndoplasmin/0.453
2om9AJAPeroxisome proliferator-activated receptor gamma/0.453
1rfvADPPyridoxal kinase2.7.1.350.452
2jedLG8Protein kinase C theta type2.7.11.130.452
2z3uCRRCytochrome P450/0.452
3a4oSTUTyrosine-protein kinase Lyn2.7.10.20.452
3s2a2NQPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.452
3sa27DRDihydrofolate reductase/0.452
4c4f7CEDual specificity protein kinase TTK2.7.12.10.452
4grb0XGCasein kinase II subunit alpha2.7.11.10.452
4lmnEUIDual specificity mitogen-activated protein kinase kinase 12.7.12.20.452
4mcv29KProto-oncogene tyrosine-protein kinase Src2.7.10.20.452
4o2bLOCTubulin beta-2B chain/0.452
1kl2FONSerine hydroxymethyltransferase/0.451
2chw039Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.451
2hy0306Serine/threonine-protein kinase Chk12.7.11.10.451
3tz3B36Acetyl-CoA carboxylase/0.451
1uvrBI83-phosphoinositide-dependent protein kinase 12.7.11.10.450
2e98B29Ditrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.450
2hog710Serine/threonine-protein kinase Chk12.7.11.10.450
3cgfJNFMitogen-activated protein kinase 102.7.11.240.450
3keuATPPyridoxal kinase2.7.1.350.450
4gyiADPUncharacterized protein/0.450
4hys1BJMitogen-activated protein kinase 82.7.11.240.450
4i3wNADAldehyde dehydrogenase (NAD+)/0.450
1dhjMTXDihydrofolate reductase1.5.1.30.449
1xl2189Gag-Pol polyprotein3.4.23.160.449
2etm7PYFocal adhesion kinase 12.7.10.20.449
2hw2RFPRifampin ADP-ribosyl transferase/0.449
2jdsL20cAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.449
3ntgD72Prostaglandin G/H synthase 21.14.99.10.449
4jia1K3Tyrosine-protein kinase JAK2/0.449
4oj4DIFPeroxisome proliferator-activated receptor gamma/0.449
4yduADPtRNA N6-adenosine threonylcarbamoyltransferase/0.449
1bygSTUTyrosine-protein kinase CSK/0.448
1r0zATPCystic fibrosis transmembrane conductance regulator/0.448
2w9sTOPDihydrofolate reductase type 1 from Tn40031.5.1.30.448
3invC50Bifunctional dihydrofolate reductase-thymidylate synthase1.5.1.30.448
4bbe3O4Tyrosine-protein kinase JAK2/0.448
4dk50KOPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.448
4kb81QNCasein kinase I isoform delta2.7.11.10.448
4l9i8PRRhodopsin kinase/0.448
1fff0Q4Gag-Pol polyprotein3.4.23.160.447
1q4u4CA4-hydroxybenzoyl-CoA thioesterase3.1.2.230.447
1wvySTUDeath-associated protein kinase 12.7.11.10.447
1ydrIQPcAMP-dependent protein kinase catalytic subunit alpha2.7.11.110.447
2cf6NAPCinnamyl alcohol dehydrogenase 51.1.1.1950.447
2hcdBIVVitamin D3 receptor A/0.447
2hk9NAPShikimate dehydrogenase (NADP(+))/0.447
2xchCKG3-phosphoinositide-dependent protein kinase 12.7.11.10.447
2y8lADP5'-AMP-activated protein kinase subunit gamma-1/0.447
3c0g3AMPeripheral plasma membrane protein CASK2.7.11.10.447
3pb3SAH16S rRNA (adenine(1408)-N(1))-methyltransferase2.1.1.1800.447
4f1sF1SPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.447
4hvi19STyrosine-protein kinase JAK32.7.10.20.447
4kbk1QGCasein kinase I isoform delta2.7.11.10.447
4otpADPSerine/threonine-protein kinase RIO12.7.11.10.447
1iwiCAMCamphor 5-monooxygenase1.14.15.10.446
1pjkANPCasein kinase II subunit alpha2.7.11.10.446
1qbgFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.446
1zthADPRIO-type serine/threonine-protein kinase Rio12.7.11.10.446
2pvhP19Casein kinase II subunit alpha2.7.11.10.446
3etgGWDGlutamate dehydrogenase 1, mitochondrial1.4.1.30.446
4awo99BHeat shock protein HSP 90-alpha/0.446
4bgePYWEnoyl-[acyl-carrier-protein] reductase [NADH]1.3.1.90.446
4en4ATPPyridoxal kinase2.7.1.350.446
4i22IREEpidermal growth factor receptor2.7.10.10.446
4k110J9Proto-oncogene tyrosine-protein kinase Src2.7.10.20.446
4l425FIRibosomal protein S6 kinase beta-12.7.11.10.446
4ubsDIFPentalenic acid synthase1.14.15.110.446
1j39UPGDNA beta-glucosyltransferase/0.445
1m13HYFNuclear receptor subfamily 1 group I member 2/0.445
2yxuATPPyridoxal kinase2.7.1.350.445
2z97CAMCamphor 5-monooxygenase1.14.15.10.445
3dxjNE6DNA-directed RNA polymerase subunit beta/0.445
3dxjNE6DNA-directed RNA polymerase subunit beta'/0.445
3jy0LYGSerine/threonine-protein kinase pim-12.7.11.10.445
3v8w0G2Tyrosine-protein kinase ITK/TSK2.7.10.20.445
4anuEM7Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.445
4e730NRMitogen-activated protein kinase 82.7.11.240.445
4h3c0YZDitrans,polycis-undecaprenyl-diphosphate synthase ((2E,6E)-farnesyl-diphosphate specific)2.5.1.310.445
4o0uADNAurora kinase A2.7.11.10.445
1jipKTN6-deoxyerythronolide B hydroxylase/0.444
1ysx4EBSerum albumin/0.444
3mg3ECHOrange carotenoid-binding protein/0.444
3ssnMVIMycinamicin VI 2''-O-methyltransferase/0.444
3uwqU5POrotidine 5'-phosphate decarboxylase/0.444
3v5j0F2Tyrosine-protein kinase ITK/TSK2.7.10.20.444
4c4h7RODual specificity protein kinase TTK2.7.12.10.444
4ezj0SCPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4fg7ATPCalcium/calmodulin-dependent protein kinase type 12.7.11.170.444
1d4aFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.443
1k6cMK1Gag-Pol polyprotein3.4.23.160.443
1kgjFL8Transthyretin/0.443
1nvtNAPShikimate dehydrogenase (NADP(+))/0.443
1rc1KT3Trifunctional purine biosynthetic protein adenosine-32.1.2.20.443
2qfxNDPIsocitrate dehydrogenase [NADP], mitochondrial1.1.1.420.443
2uxoTACHTH-type transcriptional regulator TtgR/0.443
3cd57HI3-hydroxy-3-methylglutaryl-coenzyme A reductase1.1.1.340.443
3cisATPUniversal stress protein Rv2623/0.443
3flkNAITartrate dehydrogenase/decarboxylase1.1.1.930.443
3k5uPFQAurora kinase A2.7.11.10.443
3mqe416Prostaglandin G/H synthase 21.14.99.10.443
3pxvFMNNitroreductase/0.443
3qaqQAQPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.443
4bi1ZO6Dual specificity protein kinase TTK2.7.12.10.443
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.443
4hw319GInduced myeloid leukemia cell differentiation protein Mcl-1/0.443
4i9n1E6L-lactate dehydrogenase A chain1.1.1.270.443
4j7uNAPSepiapterin reductase1.1.1.1530.443
1kbqFADNAD(P)H dehydrogenase [quinone] 11.6.5.20.442
2cd8PXICytochrome P450 monooxygenase PikC/0.442
2czfXMPOrotidine 5'-phosphate decarboxylase4.1.1.230.442
2oxtSAMGenome polyprotein/0.442
3hllI45Mitogen-activated protein kinase 14/0.442
3il1B5DGlutamate receptor 2/0.442
3inwJZBHeat shock protein HSP 90-alpha/0.442
3nwxKVSGag-Pol polyprotein3.4.23.160.442
4ewqMWLMitogen-activated protein kinase 14/0.442
4hle17VPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.442
4iwo1H4Serine/threonine-protein kinase TBK12.7.11.10.442
1lolXMPOrotidine 5'-phosphate decarboxylase4.1.1.230.441
2btdADPPEP-dependent dihydroxyacetone kinase, ADP-binding subunit DhaL2.70.441
2ft9CHDFatty acid-binding protein 2, liver/0.441
2ghlLIBMitogen-activated protein kinase 14/0.441
2hfpNSIPeroxisome proliferator-activated receptor gamma/0.441
2objVRVSerine/threonine-protein kinase pim-12.7.11.10.441
2pziAXXSerine/threonine-protein kinase PknG2.7.11.10.441
2w05FRTCyclin-dependent kinase 22.7.11.220.441
3g49NAPCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.441
3l08ZIGPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.441
3nbvANPKetohexokinase/0.441
3ofm4B0Casein kinase II subunit alpha'2.7.11.10.441
3rpr25ZCyclin-dependent kinase 22.7.11.220.441
4ctaATPCinA-like protein/0.441
4ez50RSCyclin-dependent kinase 62.7.11.220.441
4j6cSTRCytochrome P450 monooxygenase/0.441
4jx1CAHCamphor 5-monooxygenase1.14.15.10.441
4l3l5FIRibosomal protein S6 kinase beta-12.7.11.10.441
5ag6MYAGlycylpeptide N-tetradecanoyltransferase/0.441
1k6tXN1Gag-Pol polyprotein3.4.23.160.440
1yw2PGJMitogen-activated protein kinase 14/0.440
2dbrNAPGlyoxylate reductase1.1.1.260.440
2oyeIM8Prostaglandin G/H synthase 11.14.99.10.440
3at4CCKCasein kinase II subunit alpha2.7.11.10.440
3kpkFADSulfide-quinone reductase/0.440
3lu8IQXSerum albumin/0.440
3mdvCL6Cholesterol 24-hydroxylase/0.440
3vn2TLSPeroxisome proliferator-activated receptor gamma/0.440
3we45FIRibosomal protein S6 kinase beta-12.7.11.10.440
4aguD15Cyclin-dependent kinase-like 1/0.440
4anv751Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4c4iX20Dual specificity protein kinase TTK2.7.12.10.440
4ryvZEAProtein LlR18A/0.440
4xf7ACPCarbohydrate/pyrimidine kinase, PfkB family/0.440
4xumIMNPeroxisome proliferator-activated receptor gamma/0.440
5br4NADLactaldehyde reductase1.1.1.770.440