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 |
|---|---|---|---|
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Binding Site Similarity |
Align |
|---|---|---|---|---|---|
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 1.000 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.852 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.821 | |
| 2zc9 | 22U | Prothrombin | 3.4.21.5 | 0.810 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.800 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.781 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.774 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.766 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.762 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.751 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.751 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.747 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.740 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.738 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.738 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.730 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.730 | |
| 2zi2 | 24U | Prothrombin | 3.4.21.5 | 0.726 | |
| 2zda | 32U | Prothrombin | 3.4.21.5 | 0.723 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.721 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.719 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.718 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.716 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.708 | |
| 4ax9 | N5N | Prothrombin | 3.4.21.5 | 0.703 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.699 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.697 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.695 | |
| 2v3o | I26 | Prothrombin | 3.4.21.5 | 0.694 | |
| 1ype | UIP | Prothrombin | 3.4.21.5 | 0.685 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.684 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.683 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.680 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.679 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.679 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.677 | |
| 3dhk | 23U | Prothrombin | 3.4.21.5 | 0.677 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.676 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.673 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.672 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.670 | |
| 1ypg | UIR | Prothrombin | 3.4.21.5 | 0.670 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.669 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.665 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.664 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.661 | |
| 2anm | CDO | Prothrombin | 3.4.21.5 | 0.659 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.658 | |
| 1ta6 | 177 | Prothrombin | 3.4.21.5 | 0.655 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.651 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.649 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.645 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.642 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.637 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.636 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.634 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.633 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.632 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.631 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.630 | |
| 1oyt | FSN | Prothrombin | 3.4.21.5 | 0.626 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.626 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.625 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.623 | |
| 2cf8 | ESH | Prothrombin | 3.4.21.5 | 0.623 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.622 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.621 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.619 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.616 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.613 | |
| 2cf9 | 348 | Prothrombin | 3.4.21.5 | 0.612 | |
| 2jh0 | 701 | Prothrombin | 3.4.21.5 | 0.612 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.612 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.610 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.609 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.609 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.608 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.605 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.602 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.599 | |
| 2cn0 | F25 | Prothrombin | 3.4.21.5 | 0.596 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.595 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.594 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.592 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.591 | |
| 2bvs | 2CE | Prothrombin | 3.4.21.5 | 0.590 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.589 | |
| 4e7r | 0NW | Prothrombin | 3.4.21.5 | 0.584 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.582 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.578 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.576 | |
| 2gde | SN3 | Prothrombin | 3.4.21.5 | 0.572 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.572 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.563 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.549 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.543 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.538 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.523 | |
| 3egk | M18 | Prothrombin | 3.4.21.5 | 0.523 | |
| 1c4v | IH2 | Prothrombin | 3.4.21.5 | 0.522 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.520 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.513 | |
| 4ayv | 9MQ | Prothrombin | 3.4.21.5 | 0.512 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.501 | |
| 1ta2 | 176 | Prothrombin | 3.4.21.5 | 0.500 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.494 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.493 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.493 | |
| 2ign | FAD | Pyranose 2-oxidase | / | 0.488 | |
| 4gv4 | MEJ | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.488 | |
| 1uvs | I11 | Prothrombin | 3.4.21.5 | 0.487 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.486 | |
| 1ju2 | FAD | (R)-mandelonitrile lyase 2 | 4.1.2.10 | 0.484 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.484 | |
| 3ozd | 4CT | S-methyl-5'-thioadenosine phosphorylase | / | 0.482 | |
| 1j9z | FAD | NADPH--cytochrome P450 reductase | / | 0.481 | |
| 4bca | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.481 | |
| 3oqf | S51 | Renin | 3.4.23.15 | 0.480 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.478 | |
| 1mu8 | CDB | Prothrombin | 3.4.21.5 | 0.478 | |
| 3oqk | S52 | Renin | 3.4.23.15 | 0.476 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.475 | |
| 2pzj | NAD | Putative nucleotide sugar epimerase/ dehydratase | / | 0.471 | |
| 5doz | NDP | JamJ | / | 0.468 | |
| 4bc7 | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.466 | |
| 3mpj | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.465 | |
| 4b1j | A1R | Poly(ADP-ribose) glycohydrolase | 3.2.1.143 | 0.465 | |
| 3ig6 | 438 | Urokinase-type plasminogen activator | 3.4.21.73 | 0.464 | |
| 4gv0 | 8ME | Poly [ADP-ribose] polymerase 3 | 2.4.2.30 | 0.463 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.460 | |
| 4bb3 | KKA | Isopenicillin N synthase | 1.21.3.1 | 0.460 | |
| 1fml | RTL | Retinol dehydratase | / | 0.459 | |
| 1sa5 | BMV | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.458 | |
| 1x8l | OXR | Retinol dehydratase | / | 0.458 | |
| 1c7o | PPG | Hemolysin | / | 0.457 | |
| 3eku | CY9 | Actin-5C | / | 0.457 | |
| 3nu0 | 3TU | Dihydrofolate reductase | 1.5.1.3 | 0.456 | |
| 1pqc | 444 | Oxysterols receptor LXR-beta | / | 0.455 | |
| 2dvl | FAD | Acyl-CoA dehydrogenase | / | 0.455 | |
| 4gh5 | NAD | Short-chain dehydrogenase/reductase SDR | / | 0.455 | |
| 4xgu | ADP | Putative pachytene checkpoint protein 2 | / | 0.455 | |
| 2g24 | 7IG | Renin | 3.4.23.15 | 0.454 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.454 | |
| 2wu4 | HBP | Acetylcholinesterase | 3.1.1.7 | 0.454 | |
| 2g1y | 5IG | Renin | 3.4.23.15 | 0.453 | |
| 2xuh | TZ4 | Acetylcholinesterase | 3.1.1.7 | 0.453 | |
| 3eks | CY9 | Actin-5C | / | 0.453 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.453 | |
| 2zat | NAP | Dehydrogenase/reductase SDR family member 4 | 1.1.1.184 | 0.452 | |
| 3k3e | PDB | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.452 | |
| 4dbz | NDP | Putative ketoacyl reductase | 1.3.1 | 0.452 | |
| 4q71 | FAD | Bifunctional protein PutA | / | 0.452 | |
| 1kts | C24 | Prothrombin | 3.4.21.5 | 0.451 | |
| 2q1s | NAI | Putative nucleotide sugar epimerase/ dehydratase | / | 0.451 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.451 | |
| 4gxs | 0YS | Glutamate receptor 2 | / | 0.451 | |
| 3phi | NDP | Shikimate dehydrogenase (NADP(+)) | / | 0.450 | |
| 3qt6 | 2P0 | Mevalonate diphosphate decarboxylase | / | 0.450 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.449 | |
| 1hb1 | OCV | Isopenicillin N synthase | 1.21.3.1 | 0.448 | |
| 2ifa | FMN | Uncharacterized protein | / | 0.448 | |
| 3mau | EXT | Putative sphingosine-1-phosphate lyase | / | 0.448 | |
| 5eb5 | FAD | (R)-mandelonitrile lyase 1 | 4.1.2.10 | 0.448 | |
| 1nup | NMN | Nicotinamide/nicotinic acid mononucleotide adenylyltransferase 3 | / | 0.447 | |
| 2gv8 | NDP | Thiol-specific monooxygenase | 1.14.13 | 0.447 | |
| 2zev | IPE | Geranylgeranyl pyrophosphate synthase | / | 0.447 | |
| 3own | 3OW | Renin | 3.4.23.15 | 0.447 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.446 | |
| 3q7f | ED2 | Uncharacterized protein | / | 0.445 | |
| 4kby | C2E | Stimulator of interferon genes protein | / | 0.445 | |
| 2rlc | CHD | Choloylglycine hydrolase | 3.5.1.24 | 0.444 | |
| 2vbp | VB1 | Isopenicillin N synthase | 1.21.3.1 | 0.444 | |
| 3dy8 | 5GP | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.444 | |
| 3e30 | ED4 | Protein farnesyltransferase subunit beta | 2.5.1.58 | 0.444 | |
| 3g6z | A7T | Renin | 3.4.23.15 | 0.444 | |
| 3r95 | ACO | MccE protein | / | 0.444 | |
| 4f7i | NAD | 3-isopropylmalate dehydrogenase | 1.1.1.85 | 0.444 | |
| 1knr | FAD | L-aspartate oxidase | 1.4.3.16 | 0.443 | |
| 1vf3 | GDN | Glutathione S-transferase 3 | 2.5.1.18 | 0.443 | |
| 2a2x | NA9 | Prothrombin | 3.4.21.5 | 0.443 | |
| 3sqx | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.443 | |
| 4ge9 | 0L0 | Kynurenine/alpha-aminoadipate aminotransferase, mitochondrial | 2.6.1.39 | 0.443 | |
| 4uug | PXG | Branched-chain amino acid aminotransferase, putative | / | 0.443 | |
| 2v13 | C40 | Renin | 3.4.23.15 | 0.442 | |
| 3p62 | FMN | Pentaerythritol tetranitrate reductase | / | 0.442 | |
| 4f1l | 0RY | Poly [ADP-ribose] polymerase 14 | 2.4.2.30 | 0.442 | |
| 1qbg | FAD | NAD(P)H dehydrogenase [quinone] 1 | 1.6.5.2 | 0.441 | |
| 4euf | NAD | Trans-2-enoyl-CoA reductase [NADH] | / | 0.441 | |
| 2g1r | 3IG | Renin | 3.4.23.15 | 0.440 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.440 | |
| 3af1 | GDP | Pantothenate kinase | 2.7.1.33 | 0.440 | |
| 3c15 | FOK | Adenylate cyclase type 2 | / | 0.440 | |
| 3c15 | FOK | Adenylate cyclase type 5 | / | 0.440 | |
| 3zht | TD9 | Multifunctional 2-oxoglutarate metabolism enzyme | 1.2.4.2 | 0.440 | |
| 5irn | ADP | Nucleotide binding oligomerization domain containing 2 | / | 0.440 |