sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 1z6l | FAD | Polyamine oxidase FMS1 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 1z6l | FAD | Polyamine oxidase FMS1 | / | 1.000 | |
| 4gdp | FAD | Polyamine oxidase FMS1 | / | 0.637 | |
| 3bi5 | FAD | Polyamine oxidase FMS1 | / | 0.627 | |
| 3bi2 | FAD | Polyamine oxidase FMS1 | / | 0.618 | |
| 4ech | FAD | Polyamine oxidase FMS1 | / | 0.615 | |
| 3cnd | FAD | Polyamine oxidase FMS1 | / | 0.604 | |
| 3cnt | FAD | Polyamine oxidase FMS1 | / | 0.601 | |
| 1xpq | FAD | Polyamine oxidase FMS1 | / | 0.600 | |
| 3cn8 | FAD | Polyamine oxidase FMS1 | / | 0.593 | |
| 1h83 | FAD | Polyamine oxidase | 1.5.3.14 | 0.590 | |
| 1rsg | FAD | Polyamine oxidase FMS1 | / | 0.588 | |
| 4gut | FAD | Lysine-specific histone demethylase 1B | 1 | 0.561 | |
| 2hko | FAD | Lysine-specific histone demethylase 1A | 1 | 0.554 | |
| 4fwe | FAD | Lysine-specific histone demethylase 1B | 1 | 0.546 | |
| 2dw4 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.545 | |
| 4fwj | FAD | Lysine-specific histone demethylase 1B | 1 | 0.544 | |
| 2yg5 | FAD | Putrescine oxidase | / | 0.542 | |
| 2yg4 | FAD | Putrescine oxidase | / | 0.541 | |
| 2vvl | FAD | Monoamine oxidase N | 1.4.3.4 | 0.539 | |
| 4xbf | FAD | Lysine-specific histone demethylase 1A | 1 | 0.526 | |
| 2yg3 | FAD | Putrescine oxidase | / | 0.522 | |
| 3k7m | FAD | 6-hydroxy-L-nicotine oxidase | / | 0.519 | |
| 2uxx | FAJ | Lysine-specific histone demethylase 1A | 1 | 0.505 | |
| 3we0 | FAD | Lysine 2-monooxygenase | / | 0.499 | |
| 2yg7 | FAD | Putrescine oxidase | / | 0.495 | |
| 3zdn | FAD | Monoamine oxidase N | 1.4.3.4 | 0.493 | |
| 4hsu | FAD | Lysine-specific histone demethylase 1B | 1 | 0.493 | |
| 2iw5 | FAD | Lysine-specific histone demethylase 1A | 1 | 0.492 | |
| 4guu | FA9 | Lysine-specific histone demethylase 1B | 1 | 0.484 | |
| 4gur | FAD | Lysine-specific histone demethylase 1B | 1 | 0.474 | |
| 2i4p | DRH | Peroxisome proliferator-activated receptor gamma | / | 0.472 | |
| 2jbs | FMN | p-hydroxyphenylacetate 3-hydroxylase, oxygenase component | / | 0.472 | |
| 5f54 | TMP | Single-stranded-DNA-specific exonuclease | / | 0.470 | |
| 2jae | FAD | L-amino acid oxidase | / | 0.467 | |
| 2e1m | FAD | L-glutamate oxidase | / | 0.466 | |
| 1hb3 | SCV | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 2pui | ADP | Methylthioribose kinase | 2.7.1.100 | 0.465 | |
| 2vbd | V10 | Isopenicillin N synthase | 1.21.3.1 | 0.465 | |
| 4prx | ADP | DNA gyrase subunit B | / | 0.464 | |
| 1kt3 | RTL | Retinol-binding protein 4 | / | 0.462 | |
| 1qiq | ACC | Isopenicillin N synthase | 1.21.3.1 | 0.461 | |
| 4bfv | ZVV | Pantothenate kinase | 2.7.1.33 | 0.460 | |
| 1xl8 | 152 | Peroxisomal carnitine O-octanoyltransferase | 2.3.1.137 | 0.459 | |
| 2xvf | FAD | Putative flavin-containing monooxygenase | / | 0.459 | |
| 1n1e | NDE | Glycerol-3-phosphate dehydrogenase [NAD(+)], glycosomal | 1.1.1.8 | 0.458 | |
| 1kt6 | RTL | Retinol-binding protein 4 | / | 0.457 | |
| 2fja | FAD | Adenylylsulfate reductase, subunit A (AprA) | / | 0.455 | |
| 3zhq | TPP | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.455 | |
| 1q6n | P90 | Tyrosine-protein phosphatase non-receptor type 1 | 3.1.3.48 | 0.454 | |
| 2ivi | ACW | Isopenicillin N synthase | 1.21.3.1 | 0.454 | |
| 2xve | FAD | Putative flavin-containing monooxygenase | / | 0.454 | |
| 4at0 | FAD | Possible succinate dehydrogenase | / | 0.454 | |
| 4wuo | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.454 | |
| 1bwk | FMN | NADPH dehydrogenase 1 | 1.6.99.1 | 0.453 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.453 | |
| 1i5b | ANP | Chemotaxis protein CheA | 2.7.13.3 | 0.453 | |
| 2x7j | TPP | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.453 | |
| 2zru | FMN | Isopentenyl-diphosphate delta-isomerase | / | 0.453 | |
| 3cgf | JNF | Mitogen-activated protein kinase 10 | 2.7.11.24 | 0.453 | |
| 3v2u | ATP | Protein GAL3 | / | 0.453 | |
| 2gjl | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.452 | |
| 2rc6 | NAP | Ferredoxin--NADP reductase | / | 0.451 | |
| 3jsw | JAR | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.451 | |
| 4c3x | FAD | 3-ketosteroid dehydrogenase | / | 0.451 | |
| 1blz | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.450 | |
| 2h3w | HC5 | Carnitine O-acetyltransferase | 2.3.1.7 | 0.450 | |
| 2xlp | FAD | Putative flavin-containing monooxygenase | / | 0.450 | |
| 3w6u | NAP | 6-phosphogluconate dehydrogenase, NAD-binding protein | / | 0.450 | |
| 2jb4 | A14 | Isopenicillin N synthase | 1.21.3.1 | 0.449 | |
| 2y1o | T26 | UDP-N-acetylmuramoylalanine--D-glutamate ligase | 6.3.2.9 | 0.449 | |
| 4c3y | FAD | 3-ketosteroid dehydrogenase | / | 0.449 | |
| 2i4j | DRJ | Peroxisome proliferator-activated receptor gamma | / | 0.448 | |
| 2xvi | FAD | Putative flavin-containing monooxygenase | / | 0.448 | |
| 4j53 | 1J4 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.448 | |
| 3jsi | WTC | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.447 | |
| 4cjx | 9L9 | C-1-tetrahydrofolate synthase, cytoplasmic, putative | / | 0.447 | |
| 4ele | 31I | Dihydrofolate reductase | / | 0.447 | |
| 2gjn | FMN | Nitronate monooxygenase | 1.13.12.16 | 0.446 | |
| 2y3r | TRK | TamL | / | 0.446 | |
| 1fxf | MJI | Phospholipase A2, major isoenzyme | 3.1.1.4 | 0.445 | |
| 3t8o | ATP | Rhodopsin kinase | / | 0.445 | |
| 4bfu | ZVU | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 4jji | NAD | Alcohol dehydrogenase class-3 | / | 0.445 | |
| 1l2t | ATP | Uncharacterized ABC transporter ATP-binding protein MJ0796 | / | 0.444 | |
| 1rkx | NAD | CDP-D-glucose-4,6-dehydratase | / | 0.444 | |
| 2owb | 626 | Serine/threonine-protein kinase PLK1 | 2.7.11.21 | 0.444 | |
| 3slk | NDP | Polyketide synthase extender module 2 | / | 0.444 | |
| 4qi5 | FAD | Cellobiose dehydrogenase | / | 0.444 | |
| 2xlr | FAD | Putative flavin-containing monooxygenase | / | 0.443 | |
| 3zoi | M2W | Isopenicillin N synthase | 1.21.3.1 | 0.443 | |
| 4i8x | 6P3 | L-lactate dehydrogenase A chain | 1.1.1.27 | 0.443 | |
| 1bk0 | ACV | Isopenicillin N synthase | 1.21.3.1 | 0.442 | |
| 1m6i | FAD | Apoptosis-inducing factor 1, mitochondrial | 1.1.1 | 0.442 | |
| 1xdd | AAY | Integrin alpha-L | / | 0.442 | |
| 2xls | FAD | Putative flavin-containing monooxygenase | / | 0.442 | |
| 3tk3 | CPZ | Cytochrome P450 2B4 | 1.14.14.1 | 0.442 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.442 | |
| 1x1c | SAH | C-20 methyltransferase | / | 0.441 | |
| 2ojt | UBA | Glutamate receptor ionotropic, kainate 1 | / | 0.441 | |
| 3glm | COO | Glutaconyl-CoA decarboxylase alpha subunit | / | 0.441 | |
| 3kpk | FAD | Sulfide-quinone reductase | / | 0.441 | |
| 3up5 | NAP | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.441 | |
| 4tx9 | AMZ | Phosphoribosyl isomerase A | / | 0.441 | |
| 5doz | NDP | JamJ | / | 0.441 | |
| 1g6o | ADP | Cag alpha | / | 0.440 | |
| 1i5a | ACP | Chemotaxis protein CheA | 2.7.13.3 | 0.440 | |
| 1ve3 | SAM | Uncharacterized protein | / | 0.440 | |
| 1ykd | CMP | Adenylate cyclase | / | 0.440 | |
| 1zeo | C01 | Peroxisome proliferator-activated receptor gamma | / | 0.440 | |
| 2j9g | ADP | Biotin carboxylase | 6.3.4.14 | 0.440 | |
| 2q4b | NAP | Uncharacterized protein At5g02240 | / | 0.440 | |
| 2zza | FOL | Dihydrofolate reductase | / | 0.440 | |
| 3pft | FMN | Flavin reductase | / | 0.440 | |
| 3uoy | NAP | 2-oxo-Delta(3)-4,5,5-trimethylcyclopentenylacetyl-CoA monooxygenase | 1.14.13.160 | 0.440 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.440 | |
| 4heu | 15J | cAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10A | 3.1.4.17 | 0.440 | |
| 4mlp | 2CX | Cryptochrome-2 | / | 0.440 | |
| 5ej4 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.440 | |
| 5ej6 | TD6 | 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase | / | 0.440 |