Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Promising
SASA cached
Promising and worth follow-up
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
14.4 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.77, Jaccard 0.59
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
52% of hydrophobic surface appears solvent-exposed (12/23 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-0.683 kcal/mol/HA)
✓ Good fit quality (FQ -6.59)
✓ Good H-bonds (3 bonds)
✓ Deep burial (72% SASA buried)
✓ Lipophilic contacts well-matched (88%)
✗ Moderate strain (14.4 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (7)
Score
-20.488
kcal/mol
LE
-0.683
kcal/mol/HA
Fit Quality
-6.59
FQ (Leeson)
HAC
30
heavy atoms
MW
543
Da
LogP
6.80
cLogP
Final rank
2.2113
rank score
Inter norm
-0.894
normalised
Contacts
14
H-bonds 4
Interaction summary
HBD 3
HY 7
PI 0
CLASH 3
Interaction summary
HBD 3
HY 7
PI 0
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 3.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| Name | 9IFF | Contacts | 13 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA209
ARG74
ASN208
GLY214
GLY215
GLY85
LEU73
LYS211
MET70
PHE83
PRO212
PRO213
VAL88
| ||
| Current overlap | 10 | Native recall | 0.77 |
| Jaccard | 0.59 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
Protein summary
489 residues
| Protein target | T15 | Atoms | 7420 |
|---|---|---|---|
| Residues | 489 | Chains | 1 |
| Residue summary | VAL:768; LYS:704; LEU:703; ILE:532; GLU:450; THR:434; ARG:408; PHE:400; ALA:390; ASN:350; PRO:350; GLY:336; SER:319; TYR:294; ASP:264; MET:204 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 672 | 0.514679985666019 | -0.894442 | -23.4063 | 2 | 18 | 0 | 0.00 | - | - | no | Open |
| 678 | 0.8105169412196023 | -0.697208 | -16.6119 | 3 | 9 | 0 | 0.00 | - | - | no | Open |
| 674 | 2.040126377083499 | -0.900631 | -24.1106 | 3 | 19 | 0 | 0.00 | - | - | no | Open |
| 676 | 2.2112625099320904 | -0.894359 | -20.4876 | 4 | 14 | 10 | 0.77 | - | - | no | Current |
| 672 | 2.23237953245765 | -0.881443 | -23.9855 | 2 | 19 | 0 | 0.00 | - | - | no | Open |
| 674 | 2.7366679178174302 | -0.777686 | -22.0152 | 2 | 16 | 0 | 0.00 | - | - | no | Open |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-20.488kcal/mol
Ligand efficiency (LE)
-0.6829kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.588
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
543.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
6.80
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
14.45kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
40.70kcal/mol
Minimised FF energy
26.25kcal/mol
SASA & burial
✓ computed
SASA (unbound)
689.1Ų
Total solvent-accessible surface area of free ligand
BSA total
496.1Ų
Buried surface area upon binding
BSA apolar
434.5Ų
Hydrophobic contacts buried
BSA polar
61.5Ų
Polar contacts buried
Fraction buried
72.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
87.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3036.1Ų
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
4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1586.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)