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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry medium
Native strong
SASA done
Strain ΔE
15.6 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.62, Jaccard 0.44
Reason: no major geometry red flags detected
3 protein-contact clashes
3 intramolecular clashes
44% of hydrophobic surface appears solvent-exposed (11/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-0.645 kcal/mol/HA)
✓ Good fit quality (FQ -6.29)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (67% SASA buried)
✓ Lipophilic contacts well-matched (82%)
✗ Moderate strain (15.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (15)
Score
-20.002
kcal/mol
LE
-0.645
kcal/mol/HA
Fit Quality
-6.29
FQ (Leeson)
HAC
31
heavy atoms
MW
406
Da
LogP
4.85
cLogP
Interaction summary
HB 6
HY 15
PI 0
CLASH 3
⚠ Exposure 44%
Interaction summary
HB 6
HY 15
PI 0
CLASH 3
⚠ Exposure 44%
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
Partial hydrophobic solvent exposure
44% of hydrophobic surface appears solvent-exposed (11/25 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 25
Buried (contacted) 14
Exposed 11
LogP 4.85
H-bonds 6
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 2.940 | Score | -20.002 |
|---|---|---|---|
| Inter norm | -0.774 | Intra norm | 0.129 |
| Top1000 | no | Excluded | no |
| Contacts | 13 | H-bonds | 6 |
| Artifact reason | geometry warning; 15 clashes; 1 protein clash | ||
| Residues |
ALA209
ALA90
GLY214
GLY215
GLY246
LYS211
LYS216
LYS89
MET70
PRO212
PRO213
TYR210
VAL88
| ||
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 | 8 | Native recall | 0.62 |
| Jaccard | 0.44 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 429 | 0.3763685020700806 | -1.11733 | -30.2356 | 4 | 13 | 0 | 0.00 | - | - | no | Open |
| 456 | 0.8291394658452832 | -1.13404 | -36.6273 | 9 | 15 | 0 | 0.00 | - | - | no | Open |
| 460 | 1.4845961023568308 | -0.936064 | -28.1676 | 4 | 18 | 0 | 0.00 | - | - | no | Open |
| 479 | 2.2465523555658673 | -1.07372 | -31.8463 | 6 | 14 | 0 | 0.00 | - | - | no | Open |
| 478 | 2.6811516906246866 | -0.848983 | -23.9664 | 4 | 16 | 0 | 0.00 | - | - | no | Open |
| 431 | 2.7950112958399265 | -0.797896 | -16.0129 | 3 | 18 | 0 | 0.00 | - | - | no | Open |
| 531 | 2.9396166091762534 | -0.774253 | -20.0016 | 6 | 13 | 8 | 0.62 | - | - | no | Current |
| 440 | 5.900848019733364 | -0.907256 | -20.21 | 8 | 14 | 0 | 0.00 | - | - | no | Open |
| 457 | 7.7386159492059985 | -1.02476 | -29.1943 | 16 | 22 | 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
-20.002kcal/mol
Ligand efficiency (LE)
-0.6452kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.286
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
31HA
Physicochemical properties
Molecular weight
406.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
4.85
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
15.63kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
117.69kcal/mol
Minimised FF energy
102.05kcal/mol
SASA & burial
✓ computed
SASA (unbound)
672.7Ų
Total solvent-accessible surface area of free ligand
BSA total
448.1Ų
Buried surface area upon binding
BSA apolar
365.6Ų
Hydrophobic contacts buried
BSA polar
82.4Ų
Polar contacts buried
Fraction buried
66.6%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
81.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2985.6Ų
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
1593.8Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)