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 |
|---|---|---|---|
| 4baq | M4Z | Prothrombin | 3.4.21.5 |
| PDB ID | HET | Uniprot Name | EC Number | Cavity Similarity |
Align |
|---|---|---|---|---|---|
| 4baq | M4Z | Prothrombin | 3.4.21.5 | 1.000 | |
| 4ban | M6S | Prothrombin | 3.4.21.5 | 0.924 | |
| 4bam | MM9 | Prothrombin | 3.4.21.5 | 0.858 | |
| 4bak | M67 | Prothrombin | 3.4.21.5 | 0.826 | |
| 3eq0 | 2TS | Prothrombin | 3.4.21.5 | 0.761 | |
| 2zgb | 21U | Prothrombin | 3.4.21.5 | 0.745 | |
| 7kme | ACE_0BN_CHG_PRR | Prothrombin | 3.4.21.5 | 0.717 | |
| 2znk | 31U | Prothrombin | 3.4.21.5 | 0.713 | |
| 4bao | MVF | Prothrombin | 3.4.21.5 | 0.711 | |
| 2zf0 | 51U | Prothrombin | 3.4.21.5 | 0.692 | |
| 3dux | 64U | Prothrombin | 3.4.21.5 | 0.683 | |
| 2zgx | 29U | Prothrombin | 3.4.21.5 | 0.680 | |
| 2zdv | 37U | Prothrombin | 3.4.21.5 | 0.674 | |
| 4bah | MEL | Prothrombin | 3.4.21.5 | 0.673 | |
| 2bxt | C2D | Prothrombin | 3.4.21.5 | 0.652 | |
| 1zrb | 062 | Prothrombin | 3.4.21.5 | 0.648 | |
| 2zhe | 13U | Prothrombin | 3.4.21.5 | 0.645 | |
| 2zfq | 45U | Prothrombin | 3.4.21.5 | 0.640 | |
| 1nzq | 162 | Prothrombin | 3.4.21.5 | 0.639 | |
| 1k21 | IGN | Prothrombin | 3.4.21.5 | 0.634 | |
| 1afe | ALZ | Prothrombin | 3.4.21.5 | 0.633 | |
| 1zgv | 501 | Prothrombin | 3.4.21.5 | 0.630 | |
| 1t4v | 14A | Prothrombin | 3.4.21.5 | 0.621 | |
| 2r2m | I50 | Prothrombin | 3.4.21.5 | 0.619 | |
| 2zff | 53U | Prothrombin | 3.4.21.5 | 0.619 | |
| 3hat | GLY_VAL_ARG_RNG | Prothrombin | 3.4.21.5 | 0.619 | |
| 2zhq | 27U | Prothrombin | 3.4.21.5 | 0.618 | |
| 3biu | 10U | Prothrombin | 3.4.21.5 | 0.616 | |
| 1mue | CDD | Prothrombin | 3.4.21.5 | 0.613 | |
| 1z71 | L17 | Prothrombin | 3.4.21.5 | 0.613 | |
| 1mu6 | CDA | Prothrombin | 3.4.21.5 | 0.612 | |
| 1t4u | 81A | Prothrombin | 3.4.21.5 | 0.612 | |
| 4n3l | 2FN | Prothrombin | 3.4.21.5 | 0.610 | |
| 1d6w | 00R | Prothrombin | 3.4.21.5 | 0.609 | |
| 2zg0 | 50U | Prothrombin | 3.4.21.5 | 0.606 | |
| 2uuj | 896 | Prothrombin | 3.4.21.5 | 0.604 | |
| 3c1k | T15 | Prothrombin | 3.4.21.5 | 0.601 | |
| 3p17 | 99P | Prothrombin | 3.4.21.5 | 0.600 | |
| 1vzq | SHY | Prothrombin | 3.4.21.5 | 0.599 | |
| 3qto | 10P | Prothrombin | 3.4.21.5 | 0.599 | |
| 1a4w | QWE | Prothrombin | 3.4.21.5 | 0.598 | |
| 1ae8 | AZL | Prothrombin | 3.4.21.5 | 0.596 | |
| 2zfr | 46U | Prothrombin | 3.4.21.5 | 0.595 | |
| 2zhf | 49U | Prothrombin | 3.4.21.5 | 0.595 | |
| 1zgi | 382 | Prothrombin | 3.4.21.5 | 0.594 | |
| 1jwt | BLI | Prothrombin | 3.4.21.5 | 0.593 | |
| 2pks | G44 | Prothrombin | 3.4.21.5 | 0.588 | |
| 1d4p | BPP | Prothrombin | 3.4.21.5 | 0.584 | |
| 1ypl | RA8 | Prothrombin | 3.4.21.5 | 0.582 | |
| 2zhw | 12U | Prothrombin | 3.4.21.5 | 0.575 | |
| 2jh5 | 895 | Prothrombin | 3.4.21.5 | 0.572 | |
| 1sb1 | 165 | Prothrombin | 3.4.21.5 | 0.570 | |
| 1ypj | UIB | Prothrombin | 3.4.21.5 | 0.569 | |
| 3utu | 1TS | Prothrombin | 3.4.21.5 | 0.569 | |
| 1k22 | MEL | Prothrombin | 3.4.21.5 | 0.566 | |
| 1w7g | MIU | Prothrombin | 3.4.21.5 | 0.566 | |
| 3c27 | DKK | Prothrombin | 3.4.21.5 | 0.566 | |
| 2jh6 | 894 | Prothrombin | 3.4.21.5 | 0.564 | |
| 1c4u | IH1 | Prothrombin | 3.4.21.5 | 0.563 | |
| 1d3d | BZT | Prothrombin | 3.4.21.5 | 0.562 | |
| 2uuk | 897 | Prothrombin | 3.4.21.5 | 0.562 | |
| 4az2 | 9MU | Prothrombin | 3.4.21.5 | 0.562 | |
| 1ypk | CCR | Prothrombin | 3.4.21.5 | 0.561 | |
| 1bcu | PRL | Prothrombin | 3.4.21.5 | 0.559 | |
| 1d3p | BT3 | Prothrombin | 3.4.21.5 | 0.559 | |
| 4ayy | 9MX | Prothrombin | 3.4.21.5 | 0.559 | |
| 1d9i | 00P | Prothrombin | 3.4.21.5 | 0.553 | |
| 1gj5 | 130 | Prothrombin | 3.4.21.5 | 0.551 | |
| 2v3h | I25 | Prothrombin | 3.4.21.5 | 0.551 | |
| 3qtv | 06P | Prothrombin | 3.4.21.5 | 0.551 | |
| 1ghv | 120 | Prothrombin | 3.4.21.5 | 0.550 | |
| 4lxb | 7R9 | Prothrombin | 3.4.21.5 | 0.550 | |
| 5cmx | 0G6 | Prothrombin | 3.4.21.5 | 0.550 | |
| 1ypm | RA4 | Prothrombin | 3.4.21.5 | 0.545 | |
| 2bdy | UNB | Prothrombin | 3.4.21.5 | 0.545 | |
| 3qwc | 98P | Prothrombin | 3.4.21.5 | 0.545 | |
| 1xm1 | GAH | Prothrombin | 3.4.21.5 | 0.543 | |
| 2zfp | 19U | Prothrombin | 3.4.21.5 | 0.543 | |
| 1nm6 | L86 | Prothrombin | 3.4.21.5 | 0.540 | |
| 1o2g | 696 | Prothrombin | 3.4.21.5 | 0.536 | |
| 1c1u | BAI | Prothrombin | 3.4.21.5 | 0.529 | |
| 1riw | OSC | Prothrombin | 3.4.21.5 | 0.513 | |
| 1uma | IN2 | Prothrombin | 3.4.21.5 | 0.510 | |
| 3biv | 11U | Prothrombin | 3.4.21.5 | 0.508 | |
| 1o5g | CR9 | Prothrombin | 3.4.21.5 | 0.499 | |
| 3qdz | PRO_ALA_PRO_ARG | Prothrombin | 3.4.21.5 | 0.494 | |
| 3uxv | GUN | NADPH-dependent 7-cyano-7-deazaguanine reductase | / | 0.480 | |
| 3d91 | REM | Renin | 3.4.23.15 | 0.465 | |
| 3fhx | PLP | Pyridoxal kinase | 2.7.1.35 | 0.463 | |
| 1ny2 | ARG_PRO_PRO_GLY | Prothrombin | 3.4.21.5 | 0.458 | |
| 1qoq | IGP | Tryptophan synthase alpha chain | / | 0.452 | |
| 4bqz | GNP | Ectonucleoside triphosphate diphosphohydrolase 2 | / | 0.452 | |
| 2uxo | TAC | HTH-type transcriptional regulator TtgR | / | 0.450 | |
| 1lf2 | R37 | Plasmepsin-2 | 3.4.23.39 | 0.449 | |
| 2r5n | TPP | Transketolase 1 | / | 0.449 | |
| 4ntd | FAD | Thioredoxin reductase | / | 0.449 | |
| 4zu4 | 4TG | WxcM-like protein | / | 0.448 | |
| 2ziq | 26U | Prothrombin | 3.4.21.5 | 0.447 | |
| 2zvb | SAH | Precorrin-3 C17-methyltransferase | / | 0.447 | |
| 3eks | CY9 | Actin-5C | / | 0.447 | |
| 3mpi | FAD | Glutaryl-CoA dehydrogenase | 1.3.99.32 | 0.447 | |
| 2jf6 | S55 | Strictosidine-O-beta-D-glucosidase | 3.2.1.105 | 0.446 | |
| 4u03 | GTP | Cyclic GMP-AMP synthase | / | 0.446 | |
| 3sqw | ANP | ATP-dependent RNA helicase MSS116, mitochondrial | 3.6.4.13 | 0.445 | |
| 4bfx | ZVX | Pantothenate kinase | 2.7.1.33 | 0.445 | |
| 5c6c | CMP | cGMP-dependent protein kinase 2 | 2.7.11.12 | 0.445 | |
| 2ipi | AKY | Aclacinomycin-N/aclacinomycin-A oxidase | / | 0.444 | |
| 3ule | C69 | Actin-related protein 3 | / | 0.444 | |
| 4bby | FAD | Alkyldihydroxyacetonephosphate synthase, peroxisomal | 2.5.1.26 | 0.444 | |
| 1v0c | ACO | AAC(6')-Ib | / | 0.442 | |
| 2whq | HI6 | Acetylcholinesterase | 3.1.1.7 | 0.442 | |
| 2pg0 | FAD | Acyl-CoA dehydrogenase | / | 0.441 | |
| 4b1r | ITC | Tetracycline repressor protein class D | / | 0.441 | |
| 1pq9 | 44B | Oxysterols receptor LXR-beta | / | 0.440 | |
| 2g28 | TDK | Pyruvate dehydrogenase E1 component | 1.2.4.1 | 0.440 | |
| 3sxj | SAM | Putative methyltransferase | / | 0.440 |