FAIRMol

CKP-35

Pose ID 11158 Compound 3236 Pose 315

DB fairmolDocking pose analysis is being read from this database.
Compound detail Protein structures Back to compounds
Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
T17
T. brucei TR (Doorstop site) T. brucei Doorstop site
Ligand CKP-35
PDB5S9T↗

3D complex viewer

Strict H-bonds Permissive H-bonds
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising SASA cached
Promising and worth follow-up
Binding strong Geometry medium Native mixed SASA done
Strain ΔE
9.1 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.33, Jaccard 0.19, H-bond role recall 0.00
Burial
81%
Hydrophobic fit
82%
Reason: no major geometry red flags detected
5 protein-contact clashes 5 intramolecular clashes
Molecular report
Full metrics ↗
Promising Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.203 kcal/mol/HA) ✓ Good fit quality (FQ -9.64) ✓ Strong H-bond network (6 bonds) ✓ Deep burial (81% SASA buried) ✓ Lipophilic contacts well-matched (82%) ✗ Moderate strain (9.1 kcal/mol) ✗ Geometry warnings ✗ Internal clashes (7)
Score
-21.654
kcal/mol
LE
-1.203
kcal/mol/HA
Fit Quality
-9.64
FQ (Leeson)
HAC
18
heavy atoms
MW
241
Da
LogP
1.91
cLogP
Strain ΔE
9.1 kcal/mol
SASA buried
81%
Lipo contact
82% BSA apolar/total
SASA unbound
460 Ų
Apolar buried
309 Ų

Interaction summary

HB 6 HY 18 PI 1 CLASH 5

HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.

PI · π–π interactions
Native π–π recall is disabled because no explicit native π–π reference was stored.

HY · Hydrophobic contacts

CLASH · Clashes
Final rank2.151Score-21.654
Inter norm-1.293Intra norm0.073
Top1000noExcludedno
Contacts13H-bonds6
Artifact reasongeometry warning; 7 clashes; 1 protein clash
Residues
ALA284 ARG287 FAD501 GLY195 GLY197 GLY286 ILE199 ILE285 LEU332 LEU334 MET333 PHE198 SER200

Native ligand reference

★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
Name5S9TContacts12
PoseOpen native poseHB0
IFP residues
ALA365 ARG228 ARG331 GLY229 LEU332 LEU334 MET333 PHE198 PHE230 SER364 THR374 VAL366
Current overlap4Native recall0.33
Jaccard0.19RMSD-
HB strict0Strict recall0.00
HB same residue+role0HB role recall0.00
HB same residue1HB residue recall1.00

Protein summary

1033 residues
Protein targetT17Atoms15160
Residues1033Chains2
Residue summaryVAL:1536; LEU:1387; LYS:1386; ILE:1064; GLU:900; THR:868; ARG:816; PHE:800; ALA:780; ASN:700; PRO:686; GLY:672; SER:616; TYR:588; ASP:528; MET:408

Receptor context

2 kept / 0 excluded
Receptor context filtering: interactions and SASA are computed against protein atoms plus allowed cofactors/ions. Native ligand-like HETATM partners are excluded from scoring.
Kept context 2 Excluded HETATM 0
Kept cofactors / ions
A:FAD501 B:FAD501

All stored poses for this docking hit

PoseFinal rankInter normScoreHBCTCT overlapCT recallHB role rec.RMSDExcluded
251 1.7673998762122878 -1.51692 -27.3436 4 16 0 0.00 0.00 - no Open
315 2.151368131401986 -1.29284 -21.6535 6 13 4 0.33 0.00 - no Current
292 2.3410200622672233 -1.38689 -23.0391 8 16 0 0.00 0.00 - no Open

Molecular metrics

RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
✓ Metrics available

Scoring & efficiency
Docking score -21.654kcal/mol
Ligand efficiency (LE) -1.2030kcal/mol/HA
Score / heavy atom count
Fit quality (FQ) -9.641
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count 18HA

Physicochemical properties
Molecular weight 241.3Da
Lipinski: ≤ 500 Da
LogP (cLogP) 1.91
Lipinski: ≤ 5
Rotatable bonds 4

Conformational strain (MMFF94s)
Strain energy (ΔE) 9.07kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy 26.58kcal/mol
Minimised FF energy 17.52kcal/mol

SASA & burial

✓ computed
SASA (unbound) 459.8Ų
Total solvent-accessible surface area of free ligand
BSA total 374.1Ų
Buried surface area upon binding
BSA apolar 308.6Ų
Hydrophobic contacts buried
BSA polar 65.5Ų
Polar contacts buried
Fraction buried 81.4%
> 60 % indicates good pocket engagement
Lipophilic contact ratio 82.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA -6368.4Ų
SASA_nonpolar(complex) − SASA_nonpolar(receptor) − SASA_nonpolar(ligand free). Negative = non-polar surface buried upon binding. Requires full polarity-decomposed SASA computation.
Receptor non-polar SASA 8063.1Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA 2089.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)