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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Distribution of Interaction pattern similarity measured by Grim
You can zoom onto the graph by using the mouse to make a selection

Binding Modes are compared using Grim.
For more information, please see the following publication: Desaphy J. et al. Encoding Protein-Ligand Interaction Patterns in Fingerprints and Graphs J. Chem. Inf. Model., 2013, 53 (3), pp 623-637
Binding modes are considered as similar when the similarity value is greater than 0.65


Reference Protein Data Bank Entry :
PDB ID HET Uniprot Name EC Number
3qvx NAD Myo-inositol-1-phosphate synthase (Ino1)

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 1.219
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 1.140
3qvw NADMyo-inositol-1-phosphate synthase (Ino1) / 1.072
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 1.056
3qw2 NADMyo-inositol-1-phosphate synthase (Ino1) / 0.885
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.768
3cin NADMyo-inositol-1-phosphate synthase-related protein / 0.760
1x7d NADPutative ornithine cyclodeaminase / 0.757
1u7h NADPutative ornithine cyclodeaminase / 0.748
2ekl NADD-3-phosphoglycerate dehydrogenase / 0.745
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.744
1p1h NADInositol-3-phosphate synthase 5.5.1.4 0.740
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.736
1u1i NADMyo-inositol-1-phosphate synthase (Ino1) / 0.729
3ko8 NADNAD-dependent epimerase/dehydratase / 0.725
1orr NADCDP-paratose 2-epimerase / 0.721
3ids NADGlyceraldehyde-3-phosphate dehydrogenase, glycosomal 1.2.1.12 0.713
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.711
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.711
3cps NADGlyceraldehyde-3-phosphate dehydrogenase / 0.709
1pzg A3DLactate dehydrogenase / 0.708
4xqc NADHomospermidine synthase 2.5.1.44 0.706
3pdu NAPGlyoxalate/3-oxopropanoate/4-oxobutanoate reductase / 0.705
1h2b NAJNAD-dependent alcohol dehydrogenase / 0.703
3orf NADDihydropteridine reductase 1.5.1.34 0.701
1kol NADGlutathione-independent formaldehyde dehydrogenase / 0.700
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.696
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.696
2x0i NAIMalate dehydrogenase / 0.694
1pzh NADLactate dehydrogenase / 0.693
1vjt NADAlpha-glucosidase, putative / 0.693
4i1i NADMalate dehydrogenase / 0.693
2c59 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.692
4xb2 NDP319aa long hypothetical homoserine dehydrogenase / 0.692
4xrg NADHomospermidine synthase 2.5.1.44 0.691
3ec7 NADInositol 2-dehydrogenase / 0.690
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.689
1r37 NADNAD-dependent alcohol dehydrogenase 1.1.1.1 0.689
3cif NADGlyceraldehyde-3-phosphate dehydrogenase / 0.688
3uko NADAlcohol dehydrogenase class-3 / 0.688
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.688
1sow NADL-lactate dehydrogenase 1.1.1.27 0.687
1u8x NADMaltose-6'-phosphate glucosidase 3.2.1.122 0.687
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.687
2p9c NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.687
3oet NADErythronate-4-phosphate dehydrogenase / 0.687
4k28 NADShikimate dehydrogenase family protein / 0.687
2c20 NADUDP-glucose 4-epimerase / 0.686
4tvb NADHomospermidine synthase 2.5.1.44 0.685
1ie3 NADMalate dehydrogenase / 0.684
3h3j NADL-lactate dehydrogenase 1 1.1.1.27 0.683
1ky4 NADAdenosylhomocysteinase 3.3.1.1 0.682
2a92 NAIL-lactate dehydrogenase / 0.682
2pa3 NAID-3-phosphoglycerate dehydrogenase 1.1.1.95 0.682
2q1s NAIPutative nucleotide sugar epimerase/ dehydratase / 0.681
3k2b NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.680
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.679
2a94 AP0L-lactate dehydrogenase 1.1.1.27 0.678
2g76 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.677
4xq9 NADHomospermidine synthase 2.5.1.44 0.676
1ptj SNDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.675
3cmc NADGlyceraldehyde-3-phosphate dehydrogenase / 0.675
4gll NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.674
1pzf A3DLactate dehydrogenase / 0.673
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.673
3icp NADNAD-dependent epimerase/dehydratase / 0.672
4lis NADUDP-glucose 4-epimerase (Eurofung) / 0.672
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.672
2c54 NADGDP-mannose 3,5-epimerase 5.1.3.18 0.671
1bdm NAXMalate dehydrogenase / 0.670
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.670
5kjf NAJAlcohol dehydrogenase E chain 1.1.1.1 0.670
1i2b NADUDP-sulfoquinovose synthase, chloroplastic 3.13.1.1 0.669
3d64 NADAdenosylhomocysteinase / 0.669
4gdp FADPolyamine oxidase FMS1 / 0.668
4m55 NADUDP-glucuronic acid decarboxylase 1 4.1.1.35 0.668
4cpd NADAlcohol dehydrogenase / 0.667
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.666
1b3r NADAdenosylhomocysteinase 3.3.1.1 0.665
2q2q NADBeta-D-hydroxybutyrate dehydrogenase / 0.665
4b79 NADProbable short-chain dehydrogenase / 0.665
4dc1 NDPPutative ketoacyl reductase 1.3.1 0.665
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.665
3cos NADAlcohol dehydrogenase 4 1.1.1.1 0.664
3oq6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.664
4k9d NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.664
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.663
3geg NADShort-chain dehydrogenase/reductase SDR / 0.663
3keo NADRedox-sensing transcriptional repressor Rex / 0.662
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.662
3h3f NAIL-lactate dehydrogenase A chain 1.1.1.27 0.660
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.660
4yac NAIC alpha-dehydrogenase / 0.660
3l4s NADGlyceraldehyde-3-phosphate dehydrogenase 1 / 0.659
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.658
4mdh NADMalate dehydrogenase, cytoplasmic 1.1.1.37 0.658
5js6 NAD17-beta-hydroxysteroid dehydrogenase 14 1.1.1 0.658
1hdr NADDihydropteridine reductase 1.5.1.34 0.657
1y7t NDPMalate dehydrogenase / 0.657
3tqh NDPQuinone oxidoreductase / 0.657
4rvu NDPProbable quinone reductase Qor (NADPH:quinone reductase) (Zeta-crystallin homolog protein) / 0.657
1y9d FADPyruvate oxidase 1.2.3.3 0.656
2z1m NDPGDP-mannose 4,6-dehydratase / 0.656
3pym NADGlyceraldehyde-3-phosphate dehydrogenase 3 1.2.1.12 0.656
2i9p NAD3-hydroxyisobutyrate dehydrogenase, mitochondrial 1.1.1.31 0.655
3wmx NADNAD dependent epimerase/dehydratase / 0.655
1bw9 NADPhenylalanine dehydrogenase / 0.654
1mgo NADAlcohol dehydrogenase E chain 1.1.1.1 0.654
2ji7 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.654
2vyn NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.654
3aw9 NADNAD-dependent epimerase/dehydratase / 0.654
3w8d NAD3-hydroxybutyrate dehydrogenase / 0.654
5cds NAJAlcohol dehydrogenase E chain 1.1.1.1 0.654
5kcp NAJAlcohol dehydrogenase E chain 1.1.1.1 0.654
5kj6 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.654
1nqo NADGlyceraldehyde-3-phosphate dehydrogenase / 0.653
2ji6 ADPOxalyl-CoA decarboxylase 4.1.1.8 0.653
2ydx NAPMethionine adenosyltransferase 2 subunit beta / 0.653
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.653
3qrw NDPPutative ketoacyl reductase 1.3.1 0.653
4dc0 NDPPutative ketoacyl reductase 1.3.1 0.653
4e5n NADPhosphonate dehydrogenase 1.20.1.1 0.653
5cdt NAJAlcohol dehydrogenase E chain 1.1.1.1 0.653
2vhv NAIAlanine dehydrogenase 1.4.1.1 0.652
4dwv NAJAlcohol dehydrogenase E chain 1.1.1.1 0.652
2ohx NADAlcohol dehydrogenase E chain 1.1.1.1 0.651
2p5y NADUDP-glucose 4-epimerase / 0.651
2x0r NADMalate dehydrogenase / 0.651
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.651
4oaq NDPR-specific carbonyl reductase / 0.651
5g3t FDAFlavin-dependent L-tryptophan oxidase VioA / 0.651
2voj NADAlanine dehydrogenase 1.4.1.1 0.650
2yut NAPPutative short-chain oxidoreductase / 0.650
4dxh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.650
4is3 NAD3alpha-hydroxy bile acid-CoA-ester 3-dehydrogenase 2 1.17.98.1 0.650
5kcz NAJAlcohol dehydrogenase E chain 1.1.1.1 0.650
5kj1 NAJAlcohol dehydrogenase E chain 1.1.1.1 0.650