COACH-D results for job CH033577 (your_protein)

Input: Submitted protein   Submitted ligand           Output: Download all results
Predicted complex structure Click on the "eye" button in the table below to visualize the different models (the visualization is powered by 3Dmol)
spin
Current complex information Detailed information about the predicted complex on the left side
Binding sites

Rank: 1

C-Score: 0.71

TM-score: 1.00

Cluster size: 174

Protein template: 1A6W_1

Predicted binding sites: A: Y33,W92,W97
B: W33,H35,R50,K59,Y99,Y101,S105

Poseu

User submitted ligand: Submitted ligand

Docking energy: -4.1

Poset

Ligand template: NIP

Docking energy: -6.9

Sequence

>Chain A
AVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLE
>Chain B
QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKYNEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTVTVSS


Rank The predicitons are ranked by the C-Score Poseu The ligand binding pose submitted by user Poset The binding pose of the ligand obteined from the PDB template C-Score The confidence score of the prediction. C-Score ranges [0-1], where a higher score indicates a more reliable prediction Cluster size The number of protein template in a cluster P template The representative protein template in a cluster L template The representative ligand template in a cluster TM-score The structural similarity between the query and template proteins, normalized by the length of the query protein. Predicted binding residues The consensus prediciton based on spatial clustering of the binding sites from individual methods
1 0.71 174 1A6W_1 NIP 1.00 A: Y33,W92,W97
B: W33,H35,R50,K59,Y99,Y101,S105
2 0.68 109 1NC2_2 DOE 0.95 A: Y33,W92
B: W33,R50,D52,G57,K59,Y99,Y101,S105
3 0.67 89 5XCR_2 PEPTIDE 0.96 A: Y33,N35,W92
B: S31,Y32,W33,H35,R50,Y99,D100,S105,Y106
4 0.66 77 2OP4_1 EDO 0.97 A: V37,A90,W92,W97
B: H35,A97,Y99,D108,W110
5 0.62 59 1YED_2 PNB 0.92 A: Y33,N35,A90,W92,W97,F99
B: H35,V37,R50,A97,Y99,Y101,S105
Download the detailed prediction summary.    Download the templates clustering results.

   Summary of template ligands

Rank The ligands are ranked by their frequencies in the cluster
Ligand Click on the ligand ID to view more information in Q-BioLiP database and click on the download button to get the corresponding SDF file
Frequency The total number of times the ligand occurs in the cluster
PDB template The PDB structures of the ligand in the cluster. At most 20 templates are listed for each ligand.
Visualization Visualization that can be rotated and zoomed in/out with the mouse (powered by 3Dmol)
1 III 24 2ZPK_1, 2ZPK_2, 3QO0_1,
4ONG_1, 5XCR_1, 5ZIA_1,
5ZIA_3, 5ZIA_4, 5ZIA_5,
5ZIA_6, 6CDM_1, 6CDM_2,
6DC8_1, 6DCA_1, 6DCA_4,
6H06_4, 6LZ4_1, 6LZ4_2,
7BXV_1, 7RLW_2

Peptides

2 AZN 12 1OAR_1, 1OAR_2, 1OAR_3,
1OAR_4
3 HAN 9 1Y0L_1, 1Y0L_2, 1Y0L_3,
1Y0L_4, 1Y18_1, 1Y18_2,
1Y18_3, 1Y18_4
Others Other ligands in the cluster. The numbers in brackets are the frequencies. At most 100 ligands are listed.
k-mer(8), OHM(8), TNS(6), DNF(6), FUR(6), 6MD(6), ANO(5), OOX(5), STR(5), ANF(4), ANQ(4), NUC(4), TAA(4), ECO(4), HOP(3),
2M9(3), NIP(3), TES(3), NPC(3), MOI(3), 1PC(3), NPA(3), NCT(2), HAL(2), DIK(2), AB0(2), EOT(2), TCI(2), OOW(2), DOF(2),
SIH(1), XPG(1), MBT(1), T44(1), ON5(1), P4S(1), GAS(1), O2W(1), P0M(1), P2E(1), QI9(1), PME(1)

Reference

  • Q Wu, Z Peng, Y Zhang, J Yang, COACH-D: improved protein-ligand binding site prediction with refined ligand-binding poses through molecular docking, Nucleic Acids Research, 46: W438–W442 (2018).