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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
1p1h NAD Inositol-3-phosphate synthase 5.5.1.4

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
1p1h NADInositol-3-phosphate synthase 5.5.1.4 1.138
1jki NAIInositol-3-phosphate synthase 5.5.1.4 0.842
1la2 NADInositol-3-phosphate synthase 5.5.1.4 0.840
1p1i NADInositol-3-phosphate synthase 5.5.1.4 0.784
3pvz NADUDP-N-acetylglucosamine 4,6-dehydratase / 0.776
3qvx NADMyo-inositol-1-phosphate synthase (Ino1) / 0.740
5g3s FDAFlavin-dependent L-tryptophan oxidase VioA / 0.734
3ec7 NADInositol 2-dehydrogenase / 0.732
5g3t FDAFlavin-dependent L-tryptophan oxidase VioA / 0.730
4l4s NAIL-lactate dehydrogenase A chain 1.1.1.27 0.729
2gsd NADFormate dehydrogenase / 0.728
1u1i NADMyo-inositol-1-phosphate synthase (Ino1) / 0.727
4yuz S4MSpermidine synthase, putative / 0.720
1y8q ATPSUMO-activating enzyme subunit 2 6.3.2 0.719
4xrg NADHomospermidine synthase 2.5.1.44 0.715
1j5p NADL-aspartate dehydrogenase 1.4.1.21 0.714
3n7u NADFormate dehydrogenase, chloroplastic/mitochondrial / 0.713
1hyh NADL-2-hydroxyisocaproate dehydrogenase / 0.712
1x7d NADPutative ornithine cyclodeaminase / 0.712
2yg4 FADPutrescine oxidase / 0.708
2nad NADFormate dehydrogenase / 0.707
1nai NADUDP-glucose 4-epimerase 5.1.3.2 0.706
1u7h NADPutative ornithine cyclodeaminase / 0.706
3qvs NADMyo-inositol-1-phosphate synthase (Ino1) / 0.706
3qvt NAIMyo-inositol-1-phosphate synthase (Ino1) / 0.705
3nn6 FB06-hydroxy-L-nicotine oxidase / 0.703
1i8t FADUDP-galactopyranose mutase 5.4.99.9 0.699
3t37 FADPyridoxine 4-oxidase / 0.699
4mo2 FDAUDP-galactopyranose mutase / 0.699
1ib6 NADMalate dehydrogenase / 0.698
4yac NAIC alpha-dehydrogenase / 0.698
4e5k NADPhosphonate dehydrogenase 1.20.1.1 0.697
4wlu NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.697
2q1w NADPutative nucleotide sugar epimerase/ dehydratase / 0.696
4xq9 NADHomospermidine synthase 2.5.1.44 0.696
4tvb NADHomospermidine synthase 2.5.1.44 0.695
4xqc NADHomospermidine synthase 2.5.1.44 0.695
3nlc FADUncharacterized protein / 0.694
1hdr NADDihydropteridine reductase 1.5.1.34 0.693
1uxj NADMalate dehydrogenase / 0.693
3bgi SAHThiopurine S-methyltransferase 2.1.1.67 0.693
3qv1 NADGlyceraldehyde-3-phosphate dehydrogenase GAPA1, chloroplastic 1.2.1.13 0.692
2b9w FADPutative aminooxidase / 0.691
2fkn NADUrocanate hydratase 4.2.1.49 0.691
4wct FADFructosyl amine:oxygen oxidoreductase / 0.691
4yv2 S4MSpermidine synthase, putative / 0.691
2g82 NADGlyceraldehyde-3-phosphate dehydrogenase / 0.690
3qj4 FADRenalase / 0.690
4i1i NADMalate dehydrogenase / 0.690
2ign FADPyranose 2-oxidase / 0.688
2wsb NADGalactitol dehydrogenase / 0.688
3orf NADDihydropteridine reductase 1.5.1.34 0.688
4pyo SAHCatechol O-methyltransferase 2.1.1.6 0.688
4nec SAHPutative SAM-dependent methyltransferase / 0.687
1z6l FADPolyamine oxidase FMS1 / 0.686
3sxp NADADP-L-glycero-D-mannoheptose-6-epimerase / 0.686
4yag NAIC alpha-dehydrogenase / 0.686
3d64 NADAdenosylhomocysteinase / 0.685
3ru9 NADUDP-N-acetylglucosamine 4-epimerase / 0.684
4mo2 FADUDP-galactopyranose mutase / 0.684
3k4c FADPyranose 2-oxidase / 0.683
2gh5 FADGlutathione reductase, mitochondrial 1.8.1.7 0.682
3rua NADUDP-N-acetylglucosamine 4-epimerase / 0.682
3uj8 SFGPhosphoethanolamine N-methyltransferase / 0.682
1hzz NADNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.681
4j49 NADUncharacterized protein / 0.681
3jyq NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.680
1f8r FADL-amino-acid oxidase 1.4.3.2 0.679
2ba9 FADPutative aminooxidase / 0.679
2o06 MTASpermidine synthase 2.5.1.16 0.679
3nt2 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.679
1xcb NADRedox-sensing transcriptional repressor Rex / 0.678
1ywg NADGlyceraldehyde-3-phosphate dehydrogenase / 0.678
2jb1 FADL-amino acid oxidase / 0.678
3nt6 FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.678
2dfd NADMalate dehydrogenase, mitochondrial 1.1.1.37 0.677
2q7v FADThioredoxin reductase / 0.677
2yr4 FADPhenylalanine 2-monooxygenase precursor 1.13.12.9 0.677
3wv8 ATPHmd co-occurring protein HcgE / 0.676
1f8w FADNADH peroxidase 1.11.1.1 0.675
2yy7 NADL-threonine dehydrogenase / 0.675
3wv7 ADPHmd co-occurring protein HcgE / 0.675
2v7g NADUrocanate hydratase 4.2.1.49 0.674
2xve FADPutative flavin-containing monooxygenase / 0.674
3k7m FAD6-hydroxy-L-nicotine oxidase / 0.674
3s55 NADPutative short-chain dehydrogenase/reductase / 0.673
2d1y NADOxidoreductase, short-chain dehydrogenase/reductase family / 0.672
3lsi FADPyranose 2-oxidase / 0.672
3uox FAD2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase 1.14.13.160 0.672
5ccx SAHtRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A 2.1.1.220 0.672
1lld NADL-lactate dehydrogenase 2 1.1.1.27 0.671
2hms NAIKtr system potassium uptake protein A / 0.671
5ig2 NADShort-chain dehydrogenase/reductase SDR / 0.671
1qo8 FADFumarate reductase flavoprotein subunit / 0.670
2p35 SAHTrans-aconitate 2-methyltransferase / 0.670
4rtk SAHDNA adenine methylase 2.1.1.72 0.670
1mo9 FAD2-oxopropyl-CoM reductase, carboxylating 1.8.1.5 0.669
1u8x NADMaltose-6'-phosphate glucosidase 3.2.1.122 0.669
2rgh FADAlpha-Glycerophosphate Oxidase / 0.669
3jyp NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.669
3lsh FADPyranose 2-oxidase / 0.669
3nta FADFAD-dependent pyridine nucleotide-disulphide oxidoreductase / 0.669
2gdz NAD15-hydroxyprostaglandin dehydrogenase [NAD(+)] 1.1.1.141 0.668
2vou FAD2,6-dihydroxypyridine 3-monooxygenase 1.14.13.10 0.668
4jk3 NADUncharacterized protein / 0.668
1k0l FADp-hydroxybenzoate hydroxylase / 0.667
1pdh FASp-hydroxybenzoate hydroxylase / 0.667
2b9y FADPutative aminooxidase / 0.667
5a1t NAIL-lactate dehydrogenase / 0.667
1h2h NADL-aspartate dehydrogenase 1.4.1.21 0.666
1t2d NADL-lactate dehydrogenase 1.1.1.27 0.666
1zk7 FADMercuric reductase 1.16.1.1 0.666
2np7 NEAModification methylase TaqI 2.1.1.72 0.666
4plp NADHomospermidine synthase 2.5.1.44 0.666
1dhr NADDihydropteridine reductase 1.5.1.34 0.665
1gsn FADGlutathione reductase, mitochondrial 1.8.1.7 0.665
3gsi FADDimethylglycine oxidase 1.5.3.10 0.665
3i53 SAH2,7-dihydroxy-5-methyl-1-naphthoate 7-O-methyltransferase / 0.665
3icp NADNAD-dependent epimerase/dehydratase / 0.665
3jyo NADQuinate/shikimate dehydrogenase (NAD(+)) / 0.665
3oa2 NADUDP-N-acetyl-2-amino-2-deoxy-D-glucuronate oxidase / 0.665
4j2w FADKynurenine 3-monooxygenase / 0.665
1gad NADGlyceraldehyde-3-phosphate dehydrogenase A / 0.664
1jkf NADInositol-3-phosphate synthase 5.5.1.4 0.664
1p3d UMAUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.664
2r9z FADGlutathione amide reductase / 0.664
2x0r NADMalate dehydrogenase / 0.664
3grv ADNProbable ribosomal RNA small subunit methyltransferase A / 0.664
3nt4 NAIInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.664
3sm8 FNKFAD-dependent catabolic D-arginine dehydrogenase DauA / 0.664
4j43 NADUncharacterized protein / 0.664
4j49 NAIUncharacterized protein / 0.664
1szj NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.663
2bh2 SAH23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD / 0.663
2hmv ADPKtr system potassium uptake protein A / 0.663
2q1u NADPutative nucleotide sugar epimerase/ dehydratase / 0.663
3d4p NADL-lactate dehydrogenase 1 1.1.1.27 0.663
5dbj FADFADH2-dependent halogenase PltA / 0.663
1bdb NADCis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase / 0.662
1emd NADMalate dehydrogenase / 0.662
1ptj SNDNAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.662
1skm SAHModification methylase HhaI 2.1.1.37 0.662
2hnk SAHSAM-dependent O-methyltransferase / 0.662
2hu2 NADC-terminal binding protein 1 / 0.662
2zth SAMCatechol O-methyltransferase 2.1.1.6 0.662
4fp9 SAM5-methylcytosine rRNA methyltransferase NSUN4 2.1.1 0.662
4xcx SAHSmall RNA 2'-O-methyltransferase / 0.662
1il0 NADHydroxyacyl-coenzyme A dehydrogenase, mitochondrial 1.1.1.35 0.661
1p31 EPUUDP-N-acetylmuramate--L-alanine ligase 6.3.2.8 0.661
1g1a NADdTDP-glucose 4,6-dehydratase / 0.660
2dfv NADL-threonine 3-dehydrogenase / 0.660
2fn7 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.660
2ome NADC-terminal-binding protein 2 / 0.660
4nd2 A3DLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.660
4nd4 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.660
1b3r NADAdenosylhomocysteinase 3.3.1.1 0.659
1e3s NAD3-hydroxyacyl-CoA dehydrogenase type-2 1.1.1.35 0.659
1nqa NADGlyceraldehyde-3-phosphate dehydrogenase / 0.659
1sc6 NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.659
4nd3 NADLactate dehydrogenase, adjacent gene encodes predicted malate dehydrogenase / 0.659
1hku NADC-terminal-binding protein 1 1.1.1 0.658
1psd NADD-3-phosphoglycerate dehydrogenase 1.1.1.95 0.658
1geg NADDiacetyl reductase [(S)-acetoin forming] 1.1.1.304 0.657
2ore SAHDNA adenine methylase 2.1.1.72 0.657
2voj NADAlanine dehydrogenase 1.4.1.1 0.657
3p9k SAHCaffeic acid O-methyltransferase / 0.657
3sx2 NADUncharacterized protein / 0.657
5bxy SAHPutative RNA methylase family UPF0020 / 0.656
1rsg FADPolyamine oxidase FMS1 / 0.655
2yg6 FADPutrescine oxidase / 0.655
3g07 SAM7SK snRNA methylphosphate capping enzyme 2.1.1 0.655
3ntq NADInositol 2-dehydrogenase/D-chiro-inositol 3-dehydrogenase 1.1.1.18 0.655
3ruf NADUDP-N-acetylglucosamine 4-epimerase / 0.655
5lc1 NADL-threonine 3-dehydrogenase / 0.655
3ea4 FABAcetolactate synthase, chloroplastic 2.2.1.6 0.654
1l7e NAINAD(P) transhydrogenase subunit alpha part 1 1.6.1.2 0.653
2nyu SAMrRNA methyltransferase 2, mitochondrial / 0.653
1wam FADUDP-galactopyranose mutase 5.4.99.9 0.652
2oxi NADAlcohol dehydrogenase E chain 1.1.1.1 0.652
3ehe NADUDP-glucose 4-epimerase (GalE-1) / 0.652
3lov FADProtoporphyrinogen oxidase / 0.652
4j4b NAIUncharacterized protein / 0.652
5eow FAD6-hydroxynicotinate 3-monooxygenase 1.14.13.114 0.652
5jr3 SAHCarminomycin 4-O-methyltransferase DnrK 2.1.1.292 0.652
5l3d FADLysine-specific histone demethylase 1A 1 0.652
1fxs NAPGDP-L-fucose synthase / 0.651
1ht0 NADAlcohol dehydrogenase 1C 1.1.1.1 0.651
2qa2 FADPolyketide oxygenase CabE / 0.651
4c3y FAD3-ketosteroid dehydrogenase / 0.651
4nfh NAJAlcohol dehydrogenase E chain 1.1.1.1 0.651
4o59 NADGlyceraldehyde-3-phosphate dehydrogenase 1.2.1.12 0.651
5cku FADL-ornithine N(5)-monooxygenase / 0.651
1npt NADGlyceraldehyde-3-phosphate dehydrogenase / 0.650
2b9x FADPutative aminooxidase / 0.650
2o07 MTASpermidine synthase 2.5.1.16 0.650
4hb9 FADUncharacterized protein / 0.650
4jnk NAIL-lactate dehydrogenase A chain 1.1.1.27 0.650
4jq9 FADDihydrolipoyl dehydrogenase / 0.650
5cdg NAJAlcohol dehydrogenase E chain 1.1.1.1 0.650