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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
4r1l ADP Phenylacetate-coenzyme A ligase

Complex with similar interaction patterns:

PDB ID HET Uniprot Name EC Number Binding Mode
Similarity		 Align
4r1l ADPPhenylacetate-coenzyme A ligase / 0.982
4rvo ADPPhenylacetate-coenzyme A ligase / 0.816
4oxi GAPEnterobactin synthetase component F-related protein / 0.753
5ifi PRXAcetyl-coenzyme A synthetase / 0.752
1v25 ANPLong-chain-fatty-acid--CoA ligase 6.2.1.3 0.743
2p2m PRXAcetyl-coenzyme A synthetase / 0.739
1pg3 PRXAcetyl-coenzyme A synthetase / 0.736
2p2b PRXAcetyl-coenzyme A synthetase / 0.736
2p2j PRXAcetyl-coenzyme A synthetase / 0.717
3ies M24Luciferin 4-monooxygenase 1.13.12.7 0.715
2d1s SLULuciferin 4-monooxygenase 1.13.12.7 0.708
2d1t SLULuciferin 4-monooxygenase 1.13.12.7 0.696
3fce ATPD-alanine--poly(phosphoribitol) ligase subunit 1 / 0.688
3kxw 1ZZSaframycin Mx1 synthetase B / 0.687
4g37 SLULuciferin 4-monooxygenase 1.13.12.7 0.683
4g36 SLULuciferin 4-monooxygenase 1.13.12.7 0.678
2p20 PRXAcetyl-coenzyme A synthetase / 0.677
3fcc ATPD-alanine--poly(phosphoribitol) ligase subunit 1 / 0.672
3udz ADPInositol-pentakisphosphate 2-kinase 2.7.1.158 0.668
5hq8 SAHHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.664
3qwp SAMHistone-lysine N-methyltransferase SMYD3 2.1.1.43 0.662
3gpc COAAcyl-coenzyme A synthetase ACSM2A, mitochondrial 6.2.1.2 0.661
3lnv 1ZZSaframycin Mx1 synthetase B / 0.661
3fjq ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.660
4wb6 ATPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.659
3i12 ADPD-alanine--D-alanine ligase A 6.3.2.4 0.658
2zdg ADPD-alanine--D-alanine ligase / 0.657
4ib3 ADPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.657
2b9j ADPMitogen-activated protein kinase FUS3 2.7.11.24 0.656
3fhi ANPcAMP-dependent protein kinase catalytic subunit alpha 2.7.11.11 0.656
4u0o MTALipoyl synthase 2 / 0.654
2yw2 ATPPhosphoribosylamine--glycine ligase / 0.652
2p2q PRXAcetyl-coenzyme A synthetase / 0.651