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
Weak
SASA cached
Weak or marginal quality
Binding strong
Geometry high
Native strong
SASA done
Strain ΔE
12.0 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.85, Jaccard 0.61
Reason: no major geometry red flags detected
1 protein-contact clashes
36% of hydrophobic surface appears solvent-exposed (12/33 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 (-0.688 kcal/mol/HA)
✓ Good fit quality (FQ -6.99)
✓ Good burial (64% SASA buried)
✓ Lipophilic contacts well-matched (95%)
✗ Moderate strain (12.0 kcal/mol)
✗ Geometry warnings
✗ Minor protein-contact clashes (2)
✗ Many internal clashes (20)
Score
-24.759
kcal/mol
LE
-0.688
kcal/mol/HA
Fit Quality
-6.99
FQ (Leeson)
HAC
36
heavy atoms
MW
466
Da
LogP
7.87
cLogP
Interaction summary
HB 1
HY 24
PI 1
CLASH 1
⚠ Exposure 36%
Interaction summary
HB 1
HY 24
PI 1
CLASH 1
⚠ Exposure 36%
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
Partial hydrophobic solvent exposure
36% of hydrophobic surface appears solvent-exposed (12/33 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 33
Buried (contacted) 21
Exposed 12
LogP 7.87
H-bonds 1
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (6/6 atoms exposed)
| Final rank | 1.884 | Score | -24.759 |
|---|---|---|---|
| Inter norm | -0.660 | Intra norm | -0.027 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 1 |
| Artifact reason | geometry warning; 20 clashes; 2 protein contact clashes | ||
| Residues |
ALA209
ALA67
ALA90
ARG74
ASN208
GLY214
GLY215
GLY66
LEU73
LYS211
MET70
PRO212
PRO213
TYR210
TYR69
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 | 11 | Native recall | 0.85 |
| Jaccard | 0.61 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 637 | 1.8836013452383191 | -0.660271 | -24.7592 | 1 | 16 | 11 | 0.85 | - | - | no | Current |
| 620 | 3.378715481140251 | -0.78601 | -24.5487 | 3 | 14 | 0 | 0.00 | - | - | no | Open |
| 629 | 3.4909215645034988 | -0.560552 | -18.2071 | 4 | 14 | 0 | 0.00 | - | - | no | Open |
| 618 | 3.5438463176472115 | -0.703934 | -22.6562 | 3 | 19 | 0 | 0.00 | - | - | no | Open |
| 632 | 3.949263008578241 | -0.609384 | -21.8707 | 4 | 9 | 0 | 0.00 | - | - | no | Open |
| 633 | 3.986665341300043 | -0.658461 | -25.2639 | 3 | 20 | 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
-24.759kcal/mol
Ligand efficiency (LE)
-0.6878kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-6.990
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
36HA
Physicochemical properties
Molecular weight
465.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
7.87
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
12.04kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
93.88kcal/mol
Minimised FF energy
81.84kcal/mol
SASA & burial
✓ computed
SASA (unbound)
792.3Ų
Total solvent-accessible surface area of free ligand
BSA total
510.7Ų
Buried surface area upon binding
BSA apolar
484.6Ų
Hydrophobic contacts buried
BSA polar
26.1Ų
Polar contacts buried
Fraction buried
64.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
94.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-3172.4Ų
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
4005.2Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
1582.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)