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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
4rr9A3SProbable threonine--tRNA ligase 26.1.1.3

Complex with similar cavities

PDB ID HET Uniprot Name EC Number Cavity
Similarity		 Align
4rr9A3SProbable threonine--tRNA ligase 26.1.1.31.000
4rriA3TProbable threonine--tRNA ligase 26.1.1.30.648
4rrhA3SProbable threonine--tRNA ligase 26.1.1.30.629
4rrbA3TProbable threonine--tRNA ligase 26.1.1.30.627
4rrmA3TProbable threonine--tRNA ligase 26.1.1.30.627
4rr6A3SProbable threonine--tRNA ligase 26.1.1.30.622
4rr8A3SProbable threonine--tRNA ligase 26.1.1.30.622
4rr7A3SProbable threonine--tRNA ligase 26.1.1.30.608
4rrcA3TProbable threonine--tRNA ligase 26.1.1.30.607
4rrdA3TProbable threonine--tRNA ligase 26.1.1.30.602
4rrlA3SProbable threonine--tRNA ligase 26.1.1.30.592
4rrjA3SProbable threonine--tRNA ligase 26.1.1.30.575
2hl0A3SThreonine--tRNA ligase6.1.1.30.558
4rraA3TProbable threonine--tRNA ligase 26.1.1.30.553
4rrkA3TProbable threonine--tRNA ligase 26.1.1.30.542
3pd2A3SThreonine--tRNA ligase6.1.1.30.531
4xymCOAAcyl-CoA synthetase (NDP forming)/0.520
2hl2SSAThreonine--tRNA ligase6.1.1.30.519
3pd4A3GThreonine--tRNA ligase6.1.1.30.518
2hl1A3SThreonine--tRNA ligase6.1.1.30.514
4rrgA3TThreonine--tRNA ligase6.1.1.30.514
4rrrA3TThreonine--tRNA ligase6.1.1.30.499
4rrqA3SThreonine--tRNA ligase6.1.1.30.494
3pd5TSBThreonine--tRNA ligase6.1.1.30.489
3pd3A3TThreonine--tRNA ligase6.1.1.30.488
3u9fCLMChloramphenicol acetyltransferase2.3.1.280.487
4rrfA3SThreonine--tRNA ligase6.1.1.30.485
3dysIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.484
1nhz486Glucocorticoid receptor/0.483
5hbrCOAAcyl-CoA synthetase (NDP forming)/0.479
3gluLYS_VAL_METNAD-dependent protein deacetylase sirtuin-3, mitochondrial3.5.10.476
3k3hBYEHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.472
3dy8IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.469
3g493G4Corticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.469
4gdy0X1Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial2.6.1.390.469
3k3ePDBHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.468
1x8lOXRRetinol dehydratase/0.467
3b9lAZZSerum albumin/0.467
3h3t16HCollagen type IV alpha-3-binding protein/0.466
3pwhZMAAdenosine receptor A2a/0.465
4pnmNU1Tankyrase-22.4.2.300.464
3inrGDUUDP-galactopyranose mutase5.4.99.90.463
3jsiWTCHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
3jswJARHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.463
2a4nCOAAac(6')-Ii protein/0.462
3g1rNAP3-oxo-5-beta-steroid 4-dehydrogenase/0.462
4qzuRTLRetinol-binding protein 2/0.462
3vt8YI3Vitamin D3 receptor/0.460
4wdb2AM2',3'-cyclic-nucleotide 3'-phosphodiesterase3.1.4.370.460
2fk8SAMHydroxymycolate synthase MmaA42.1.10.458
3exhTPPPyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial1.2.4.10.458
3exhTPPPyruvate dehydrogenase E1 component subunit beta, mitochondrial1.2.4.10.458
3vt7VDXVitamin D3 receptor/0.458
1ddtAPUDiphtheria toxin/0.457
3h3qH13Collagen type IV alpha-3-binding protein/0.456
3tk3CPZCytochrome P450 2B41.14.14.10.456
2g1r3IGRenin3.4.23.150.455
3pqbVGPPutative oxidoreductase/0.455
1kqwRTLCellular retinol-binding protein type II/0.454
2po7CHDFerrochelatase, mitochondrial4.99.1.10.454
2qd3CHDFerrochelatase, mitochondrial4.99.1.10.454
2yy2IBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4e907RGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
4g2l0WLHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.454
1ppjANYCytochrome b/0.453
2g1n1IGRenin3.4.23.150.453
2j9fTHV2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial1.2.4.40.453
2j9fTHV2-oxoisovalerate dehydrogenase subunit beta, mitochondrial1.2.4.40.453
2xvw9NRSerum albumin/0.453
3h3r14HCollagen type IV alpha-3-binding protein/0.453
3pm1ETHTH-type transcriptional regulator QacR/0.453
4i6gFADCryptochrome-2/0.453
3up3XCAaceDAF-12/0.452
4g1z0VPVitamin D3 receptor A/0.452
4iteTEYVitamin D3 receptor/0.452
4r81FMNPredicted NADH dehydrogenase/0.451
4xsvC5PEthanolamine-phosphate cytidylyltransferase2.7.7.140.451
2pnjCHDFerrochelatase, mitochondrial4.99.1.10.450
3akn11DFatty acid-binding protein, intestinal/0.450
3lz6A0DCorticosteroid 11-beta-dehydrogenase isozyme 11.1.1.1460.450
4kxjP34Nucleoprotein/0.450
2e9uA25Serine/threonine-protein kinase Chk12.7.11.10.449
2lbaCHOFatty acid binding protein 6/0.449
3dynPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
3elm24FCollagenase 33.4.240.449
3oqkS52Renin3.4.23.150.449
4b8zGDPGDP-L-fucose synthase1.1.1.2710.449
4g2j0WFHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.449
2op18PCEnoyl-ACP reductase/0.448
2vtdLKMUDP-N-acetylmuramoylalanine--D-glutamate ligase6.3.2.90.448
3dyqPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.448
4ead0NPThymidine phosphorylase2.4.2.40.448
3q7fED2Uncharacterized protein/0.447
1rkhVD2Vitamin D3 receptor/0.446
1xp6AIUEstrogen receptor/0.446
2xlpFADPutative flavin-containing monooxygenase/0.446
2xvv9DNSerum albumin/0.446
3vswR31Renin3.4.23.150.446
4lsjLSJGlucocorticoid receptor/0.446
3gwfFADCyclohexanone monooxygenase/0.445
4nbiD3YD-tyrosyl-tRNA(Tyr) deacylase/0.445
1opbRETRetinol-binding protein 2/0.444
1x1aSAMC-20 methyltransferase/0.444
3dylPCGHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.444
3h3sH15Collagen type IV alpha-3-binding protein/0.444
3junAKDPhenazine biosynthesis protein A/B/0.444
1dtpAPUDiphtheria toxin/0.443
3gy9COAGCN5-related N-acetyltransferase/0.443
4itfTFYVitamin D3 receptor/0.443
3a783EVVitamin D3 receptor/0.442
3hxdBD7Geranylgeranyl transferase type-2 subunit beta2.5.1.600.442
3ns2PYVAbscisic acid receptor PYL2/0.442
4l1xNAPAldo-keto reductase family 1 member C2/0.442
4psbGA3Cytokinin-specific binding protein/0.442
2fpcSCGStrictosidine synthase4.3.3.20.441
2vq7FADPutative flavin-containing monooxygenase/0.441
2xuiTZ5Acetylcholinesterase3.1.1.70.441
3gwfNAPCyclohexanone monooxygenase/0.441
3n3zIBMHigh affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A/0.441
3v0o4GWHisto-blood group ABO system transferase/0.441
4i8vBHFCytochrome P450 1A11.14.14.10.441
4tjy3GNTankyrase-22.4.2.300.441
2j3qTFLAcetylcholinesterase3.1.1.70.440
2vn1FK5Peptidylprolyl isomerase/0.440
3ksqZ96Protein farnesyltransferase subunit beta2.5.1.580.440
3uicNADEnoyl-[acyl-carrier-protein] reductase [NADH]/0.440
3w0yDS4Vitamin D3 receptor/0.440
4fvz4KJNitric oxide synthase, brain1.14.13.390.440