Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
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 strong
SASA done
Strain ΔE
10.6 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.69, Jaccard 0.56
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
40% of hydrophobic surface appears solvent-exposed (6/15 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Promising
Reasonable quality metrics. Warrants further investigation.
✓ Excellent LE (-1.119 kcal/mol/HA)
✓ Good fit quality (FQ -9.54)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Moderate strain (10.6 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-23.495
kcal/mol
LE
-1.119
kcal/mol/HA
Fit Quality
-9.54
FQ (Leeson)
HAC
21
heavy atoms
MW
286
Da
LogP
2.28
cLogP
Interaction summary
HB 8
HY 9
PI 0
CLASH 5
⚠ Exposure 40%
Interaction summary
HB 8
HY 9
PI 0
CLASH 5
⚠ Exposure 40%
Partial hydrophobic solvent exposure
40% of hydrophobic surface appears solvent-exposed (6/15 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 15
Buried (contacted) 9
Exposed 6
LogP 2.28
H-bonds 8
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 3.728 | Score | -23.495 |
|---|---|---|---|
| Inter norm | -1.131 | Intra norm | 0.012 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 8 |
| Artifact reason | geometry warning; 9 clashes; 2 protein clashes | ||
| Residues |
ARG74
ASN208
ASN245
ASP71
GLY214
GLY215
GLY246
LEU73
LYS211
MET70
PRO212
PRO213
| ||
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 | ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| 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 | 9 | Native recall | 0.69 |
| Jaccard | 0.56 | RMSD | - |
| HB strict | 0 | Strict recall | - |
| HB same residue+role | 0 | HB role recall | - |
| HB same residue | 0 | HB residue recall | - |
HB · H-bonds
Mode: strict. Count shows atom-level H-bonds; unique residues in summary: 0.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 432 | 1.222860932044016 | -1.53558 | -29.3424 | 10 | 17 | 0 | 0.00 | - | - | no | Open |
| 507 | 2.8658798137281876 | -1.3035 | -24.8475 | 6 | 17 | 0 | 0.00 | - | - | no | Open |
| 464 | 2.896089366624946 | -1.21353 | -24.2204 | 8 | 14 | 0 | 0.00 | - | - | no | Open |
| 473 | 2.991356188843517 | -1.35257 | -28.5222 | 12 | 14 | 0 | 0.00 | - | - | no | Open |
| 447 | 3.4604292682728732 | -1.15154 | -23.9773 | 9 | 11 | 0 | 0.00 | - | - | no | Open |
| 446 | 3.547725783304717 | -1.35351 | -28.2583 | 6 | 16 | 0 | 0.00 | - | - | no | Open |
| 533 | 3.728277754062 | -1.13114 | -23.4955 | 8 | 12 | 9 | 0.69 | - | - | no | Current |
| 418 | 3.7308293894761544 | -1.61054 | -34.097 | 11 | 12 | 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
-23.495kcal/mol
Ligand efficiency (LE)
-1.1188kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.543
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
286.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.28
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
10.64kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
78.90kcal/mol
Minimised FF energy
68.26kcal/mol
SASA & burial
✓ computed
SASA (unbound)
475.7Ų
Total solvent-accessible surface area of free ligand
BSA total
325.8Ų
Buried surface area upon binding
BSA apolar
210.5Ų
Hydrophobic contacts buried
BSA polar
115.3Ų
Polar contacts buried
Fraction buried
68.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2776.9Ų
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
1556.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)