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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
4c5bADPD-alanine--D-alanine ligase B6.3.2.4

Complex with similar binding sites

PDB ID HET Uniprot Name EC Number Binding Site
Similarity		 Align
4c5bADPD-alanine--D-alanine ligase B6.3.2.41.000
4c5cATPD-alanine--D-alanine ligase B6.3.2.40.572
5bpfADPD-alanine--D-alanine ligase/0.553
4fflADPUncharacterized protein/0.526
2pywADPMethylthioribose kinase2.7.1.1000.525
1cm8ANPMitogen-activated protein kinase 12/0.512
1pk8ATPSynapsin-1/0.500
3wo0ADPAlanine--anticapsin ligase/0.492
1px2ATPSynapsin-1/0.486
4ezk0SDPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.480
3q5iANPProtein kinase, putative/0.478
5c1pADPD-alanine--D-alanine ligase/0.478
4fad0TBPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.474
3qtsX46Cyclin-dependent kinase 22.7.11.220.471
3ml8ML8Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.470
4feq0T8Tyrosine-protein kinase receptor TYRO32.7.10.10.470
2e9n76ASerine/threonine-protein kinase Chk12.7.11.10.469
3c4zADPRhodopsin kinase/0.468
3gu5ANPDeath-associated protein kinase 12.7.11.10.468
3r8vZ62Cyclin-dependent kinase 22.7.11.220.467
4zgnATPCell division cycle protein 123/0.465
2chx090Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.463
4ei40Q2Tyrosine-protein kinase JAK1/0.461
3wnzADPAlanine--anticapsin ligase/0.460
1g28FMNPHY3/0.459
1zthADPRIO-type serine/threonine-protein kinase Rio12.7.11.10.459
2b9fADPMitogen-activated protein kinase FUS32.7.11.240.459
1e8zSTUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.456
1fvt106Cyclin-dependent kinase 22.7.11.220.456
3r8uZ31Cyclin-dependent kinase 22.7.11.220.456
2x1nX1NCyclin-dependent kinase 22.7.11.220.455
3orpAGSSerine/threonine protein kinase/0.455
4bkz1WSMaternal embryonic leucine zipper kinase2.7.11.10.455
4ful0VUPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.454
1msmJE2Gag-Pol polyprotein3.4.23.160.453
3zcw4A2Kinesin-like protein KIF11/0.453
1sguMK1Gag-Pol polyprotein3.4.23.160.452
2r3tG4GGag-Pol polyprotein3.4.23.160.452
3mtfA3FActivin receptor type-12.7.11.300.452
3vpbADPGlutamate--LysW ligase ArgX6.3.20.452
3wo1ADPAlanine--anticapsin ligase/0.452
3datMTXDihydrofolate reductase/0.451
4acm7YGCyclin-dependent kinase 22.7.11.220.451
4eomATPCyclin-dependent kinase 22.7.11.220.451
4kd11QKCyclin-dependent kinase 22.7.11.220.451
5fdg0N8Polymerase acidic protein/0.451
1oguST8Cyclin-dependent kinase 22.7.11.220.450
1sze173Cytochrome b2, mitochondrial1.1.2.30.450
1xmmM7Gm7GpppX diphosphatase3.6.1.590.450
3my5RFZCyclin-dependent kinase 22.7.11.220.450
4dk50KOPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.450
4ftr5HKSerine/threonine-protein kinase Chk12.7.11.10.450
2izrBRKCasein kinase I isoform gamma-32.7.11.10.449
2nnqT4BFatty acid-binding protein, adipocyte/0.449
3apfBMWPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
3nrrD16Bifunctional dihydrofolate reductase-thymidylate synthase/0.449
3tkiS25Serine/threonine-protein kinase Chk12.7.11.10.449
4aw0ATP3-phosphoinositide-dependent protein kinase 12.7.11.10.449
4hvb19PPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.449
1kzkJE2Gag-Pol polyprotein3.4.23.160.448
2pz5ACPFibroblast growth factor receptor 2/0.448
3c4wATPRhodopsin kinase/0.448
3eem53VUncharacterized protein/0.448
3gytDL4Nuclear hormone receptor of the steroid/thyroid hormone receptors superfamily/0.448
3r9dX6BCyclin-dependent kinase 22.7.11.220.448
3zdfNADGlyceraldehyde-3-phosphate dehydrogenase/0.448
1c6x3INProtease/0.447
1sxjADPReplication factor C subunit 5/0.447
2pqzG0GGag-Pol polyprotein3.4.23.160.447
3gu7ADPDeath-associated protein kinase 12.7.11.10.447
3thrC2FGlycine N-methyltransferase2.1.1.200.447
4elg52JDihydrofolate reductase/0.447
2gejGDDPhosphatidyl-myo-inositol mannosyltransferase2.4.1.570.446
2p0aANPSynapsin-3/0.446
3rv3ADPBiotin carboxylase6.3.4.140.446
4bgg844Activin receptor type-12.7.11.300.446
4dcaADPAminoglycoside phosphotransferase/0.446
4u0mGTPCyclic GMP-AMP synthase/0.446
4wh3ATPN-acetylhexosamine 1-kinase2.7.1.1620.446
2i0y5CNMacrophage colony-stimulating factor 1 receptor2.7.10.10.445
3kp4MIITranscriptional regulator TcaR/0.445
3orlAGSSerine/threonine protein kinase/0.445
4azwATPO-antigen chain terminator bifunctional methyltransferase/kinase WbdD/0.445
4hyp1A1DNA gyrase subunit B/0.445
1uu7BI23-phosphoinositide-dependent protein kinase 12.7.11.10.444
1z1rHBHGag-Pol polyprotein3.4.23.160.444
2pmlANPUncharacterized protein/0.444
2v4lABJPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
3g8dADPBiotin carboxylase6.3.4.140.444
3i6oGR6Gag-Pol polyprotein3.4.23.160.444
3qarQARPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.444
4duhRLIDNA gyrase subunit B/0.444
4eepFMNPhototropin-22.7.11.10.444
4y12AGSSerine/threonine-protein kinase PknG2.7.11.10.444
1hihC20Gag-Pol polyprotein/0.443
2bycFMNBlue-light receptor of the BLUF-family/0.443
2pwrG4GGag-Pol polyprotein3.4.23.160.443
2w4jADPDeath-associated protein kinase 12.7.11.10.443
5bp9SAHPutative methyltransferase protein/0.443
1cs4GSPGuanine nucleotide-binding protein G(s) subunit alpha isoforms short/0.442
2o1xTDP1-deoxy-D-xylulose-5-phosphate synthase2.2.1.70.442
2pg0FADAcyl-CoA dehydrogenase/0.442
2r3q5SCCyclin-dependent kinase 22.7.11.220.442
3s1cZIRCytokinin dehydrogenase 11.5.99.120.442
4bqyFNTEgl nine homolog 1/0.442
4ehzJAKTyrosine-protein kinase JAK1/0.442
2bqvA1AProtease/0.441
4u9yCOAAlpha-tubulin N-acetyltransferase 1/0.441
4ww4ADPRuvB-like helicase/0.441
1e7vLY2Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
1hckATPCyclin-dependent kinase 22.7.11.220.440
1jtuLYBThymidylate synthase/0.440
1zarADPRIO-type serine/threonine-protein kinase Rio22.7.11.10.440
2ydfIO3Serum albumin/0.440
3ijdC2FMethylenetetrahydrofolate reductase/0.440
3l08ZIGPhosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit gamma isoform2.7.1.1530.440
4e1z0MXNon-receptor tyrosine-protein kinase TYK22.7.10.20.440
4hhdFMNPhototropin-12.7.11.10.440
4zhxC1V5'-AMP-activated protein kinase catalytic subunit alpha-2/0.440
4zhxC1V5'-AMP-activated protein kinase subunit beta-1/0.440