sc-PDB
An Annotated Database of Druggable Binding Sites from the Protein DataBank
An Annotated Database of Druggable Binding Sites from the Protein DataBank
Cavities 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
| PDB ID | HET | Uniprot Name | EC Number |
|---|---|---|---|
| 4ban | M6S | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4ban | M6S | Prothrombin | 3.4.21.5 | 1.000 | |
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 0.943 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.869 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.856 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.766 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.763 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.752 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.746 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.732 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.723 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.705 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.695 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.695 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.689 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.672 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.669 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.667 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.666 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.665 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.664 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.657 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.655 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.645 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.641 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.636 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.634 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.629 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.627 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.625 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.625 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.619 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.618 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.618 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.618 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.617 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.615 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.614 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.614 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.611 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.611 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.610 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.608 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.605 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.603 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.603 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.601 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.600 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.598 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.598 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.597 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.592 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.592 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.589 | |
| 1c4y | IH3 | Prothrombin | 3.4.21.5 | 0.588 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.586 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.583 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.583 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.582 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.581 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.581 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.580 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.578 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.575 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.574 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.572 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.570 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.569 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.569 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.565 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.562 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.557 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.557 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.554 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.551 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.551 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.551 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.549 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.549 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.544 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.539 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.537 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.532 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.524 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.519 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.519 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.509 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.502 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.475 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.460 | |
| 3c36 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.459 | |
| 3f68 | 91U | Prothrombin | 3.4.21.5 | 0.457 | |
| 4e90 | 7RG | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.457 | |
| 3k3h | BYE | High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A | / | 0.456 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.455 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.453 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.453 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.453 | |
| 3ou2 | SAH | SAM-dependent methyltransferase | / | 0.452 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.452 | |
| 4bqz | GNP | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.452 | |
| 2r8p | T6F | Transketolase 1 | / | 0.451 | |
| 3c35 | KAI | Glutamate receptor ionotropic, kainate 1 | / | 0.451 | |
| 3iu7 | FCD | Methionine aminopeptidase 2 | / | 0.451 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.451 | |
| 5fd8 | A5A | Putative carboxypeptidase yocD | / | 0.451 | |
| 3gjw | GJW | Poly [ADP-ribose] polymerase 1 | 2.4.2.30 | 0.450 | |
| 4h6p | FMN | Chromate reductase | / | 0.449 | |
| 1o0d | 163 | Prothrombin | 3.4.21.5 | 0.448 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.448 | |
| 1c3x | 8IG | Purine nucleoside phosphorylase | 2.4.2.1 | 0.447 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.447 | |
| 2zu8 | GDD | Mannosyl-3-phosphoglycerate synthase | 2.4.1.217 | 0.447 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.447 | |
| 4jtq | NAP | Aldo-keto reductase family 1 member C2 | / | 0.447 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.446 | |
| 2z95 | NDP | GDP-mannose 4,6-dehydratase | / | 0.446 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.445 | |
| 2hdj | NDP | Aldo-keto reductase family 1 member C2 | / | 0.445 | |
| 2jf6 | S55 | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.445 | |
| 2wf1 | ZY1 | Beta-secretase 1 | 3.4.23.46 | 0.445 | |
| 1c5n | ESI | Prothrombin | 3.4.21.5 | 0.444 | |
| 2hej | NDP | Aldo-keto reductase family 1 member C21 | 1.1.1 | 0.443 | |
| 2r5n | TPP | Transketolase 1 | / | 0.442 | |
| 3s7b | NH5 | N-lysine methyltransferase SMYD2 | / | 0.442 | |
| 4emd | C5P | 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase | / | 0.442 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.442 | |
| 2gyw | OBI | Acetylcholinesterase | 3.1.1.7 | 0.441 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.441 | |
| 3bg7 | FAD | Pyranose 2-oxidase | / | 0.441 | |
| 3v0p | 4GW | Histo-blood group ABO system transferase | / | 0.441 | |
| 4loy | 6XS | Prothrombin | 3.4.21.5 | 0.441 | |
| 1xds | DRA | Aclacinomycin 10-hydroxylase RdmB | 4.1.1 | 0.440 |