PDB-code
| Kinase structure | |
| Kinase: | MAPK13 (p38d) |
| Family: | MAPK |
| Group: | CMGC |
| Species: | HUMAN |
| IUPHAR/BPS ID: | 1502 |
| PDB: | 5EKO |
| sc-PDB: | |
| KIDFamMap: | Search |
| Release date: | 2016-07-06 |
| PubMed: | 27369736 |
| Chain: | A |
| Orthosteric ligand: | N17 |
 | |
| Structural information | |
| DFG conformation: | in |
| αC-helix conformation: | in |
| G-rich loop angle (distance): | 60.8° (18.4Å) |
| G-rich loop rotation: | 47.4° |
| Quality Score: | 7.6 |
| Resolution: | 2 Å |
| Missing Residues: | 1 |
| Missing Atoms: | 0 |
| Ligand binding mode | ||||
| Pockets | Subpockets | Waters | ||
| front gate | BP-I-A BP-I-B BP-II-in | Cluster I7 | Ligand No | Protein Yes |
| Pocket alignment | |
| Uniprot sequence: | THVGSGAYGSVCSVAIKKLRAYRELLLLKHMQENVIGLLDVYLVMPFMQ-TDLQKIMGMYIHSAGVVHRDLKPGNLAVILDFGLA |
| Sequence structure: | THVGSGAYGSVCSVAIKKLRAYRELLLLKHMQENVIGLLDVYLVMPFMQ_TDLQKIMGMYIHSAGVVHRDLKPGNLAVILDFGL_ |
| Ligand affinity | |
| ChEMBL ID: | CHEMBL3931843 |
| Bioaffinities: | 2 records for 1 kinase |
| Species | Kinase (ChEMBL naming) | Median | Min | Max | Type | Records |
|---|---|---|---|---|---|---|
| Homo sapiens | MAP kinase p38 delta | 4.8 | 4.8 | 5 | pIC50 | 2 |
Kinase-ligand interaction pattern
• Hydrophobic • Aromatic face-to-face • Aromatic face-to-edge • H-bond donor • H-bond acceptor • Ionic positive • Ionic negative
| I | g.l | II | III | αC | |||||||||||||||
| 1 T 29 | 2 H 30 | 3 V 31 | 4 G 32 | 5 S 33 | 6 G 34 | 7 A 35 | 8 Y 36 | 9 G 37 | 10 S 38 | 11 V 39 | 12 C 40 | 13 S 41 | 14 V 51 | 15 A 52 | 16 I 53 | 17 K 54 | 18 K 55 | 19 L 56 | 20 R 68 |
| • | • | • | • | • | • | ||||||||||||||
| αC | b.l | IV | |||||||||||||||||
| 21 A 69 | 22 Y 70 | 23 R 71 | 24 E 72 | 25 L 73 | 26 L 74 | 27 L 75 | 28 L 76 | 29 K 77 | 30 H 78 | 31 M 79 | 32 Q 80 | 33 E 82 | 34 N 83 | 35 V 84 | 36 I 85 | 37 G 86 | 38 L 87 | 39 L 88 | 40 D 89 |
| •• | • | • | • | ||||||||||||||||
| IV | V | GK | hinge | linker | αD | αE | |||||||||||||
| 41 V 90 | 42 Y 104 | 43 L 105 | 44 V 106 | 45 M 107 | 46 P 108 | 47 F 109 | 48 M 110 | 49 Q 111 | 50 _ _ | 51 T 112 | 52 D 113 | 53 L 114 | 54 Q 115 | 55 K 116 | 56 I 117 | 57 M 118 | 58 G 119 | 59 M 120 | 60 Y 140 |
| • | • | • | •• | ||||||||||||||||
| αE | VI | c.l | VII | VIII | x | ||||||||||||||
| 61 I 141 | 62 H 142 | 63 S 143 | 64 A 144 | 65 G 145 | 66 V 146 | 67 V 147 | 68 H 148 | 69 R 149 | 70 D 150 | 71 L 151 | 72 K 152 | 73 P 153 | 74 G 154 | 75 N 155 | 76 L 156 | 77 A 157 | 78 V 158 | 79 I 166 | 80 L 167 |
| • | |||||||||||||||||||
| DFG | a.l | ||||||||||||||||||
| 81 D 168 | 82 F 169 | 83 G 170 | 84 L 171 | 85 _ _ | |||||||||||||||
| •• | •• | • | |||||||||||||||||
Interaction pattern search
Search KLIFS for kinase-ligand complexes with similar interaction patterns:
