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 high
Native strong
SASA done
Strain ΔE
21.7 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.62, Jaccard 0.38
Reason: no major geometry red flags detected
2 protein-contact clashes
38% of hydrophobic surface appears solvent-exposed (8/21 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 (-0.911 kcal/mol/HA)
✓ Good fit quality (FQ -8.79)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ High strain energy (21.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-27.327
kcal/mol
LE
-0.911
kcal/mol/HA
Fit Quality
-8.79
FQ (Leeson)
HAC
30
heavy atoms
MW
425
Da
LogP
3.15
cLogP
Interaction summary
HB 6
HY 16
PI 0
CLASH 2
⚠ Exposure 38%
Interaction summary
HB 6
HY 16
PI 0
CLASH 2
⚠ Exposure 38%
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
38% of hydrophobic surface appears solvent-exposed (8/21 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 21
Buried (contacted) 13
Exposed 8
LogP 3.15
H-bonds 6
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (2 atoms exposed)
| Final rank | 2.626 | Score | -27.327 |
|---|---|---|---|
| Inter norm | -0.792 | Intra norm | -0.119 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 6 |
| Artifact reason | geometry warning; 11 clashes; 1 protein clash; moderate strain Δ 21.7 | ||
| Residues |
ALA209
ALA244
ALA90
ARG74
ASN208
ASN245
GLY246
LYS211
LYS89
MET70
PRO187
PRO212
PRO213
TYR210
TYR408
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 | 0.38 | 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 551 | 0.7863990384040856 | -1.0689 | -34.3256 | 10 | 13 | 0 | 0.00 | - | - | no | Open |
| 540 | 2.01639219542086 | -0.846568 | -22.4366 | 9 | 19 | 0 | 0.00 | - | - | no | Open |
| 597 | 2.6257543792701297 | -0.791858 | -27.3268 | 6 | 16 | 8 | 0.62 | - | - | no | Current |
| 552 | 2.841916052752017 | -1.32572 | -41.1595 | 11 | 19 | 0 | 0.00 | - | - | no | Open |
| 543 | 2.925843509730519 | -1.38782 | -43.7879 | 9 | 19 | 0 | 0.00 | - | - | no | Open |
| 577 | 3.073966426611157 | -0.901 | -28.5624 | 12 | 17 | 0 | 0.00 | - | - | no | Open |
| 554 | 3.391884301661245 | -0.86851 | -30.1896 | 8 | 19 | 0 | 0.00 | - | - | no | Open |
| 566 | 3.7897586704157433 | -0.890481 | -21.4571 | 10 | 12 | 0 | 0.00 | - | - | no | Open |
| 571 | 4.379321273351954 | -0.866284 | -27.1145 | 5 | 17 | 0 | 0.00 | - | - | no | Open |
| 577 | 4.446355622158319 | -0.795751 | -23.7085 | 6 | 19 | 0 | 0.00 | - | - | no | Open |
| 556 | 4.761776816752896 | -0.850102 | -27.284 | 9 | 14 | 0 | 0.00 | - | - | no | Open |
| 566 | 4.827703850716491 | -1.36608 | -35.1918 | 12 | 19 | 0 | 0.00 | - | - | no | Open |
| 581 | 5.166757877468878 | -0.708586 | -24.5919 | 8 | 14 | 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
-27.327kcal/mol
Ligand efficiency (LE)
-0.9109kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-8.787
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
425.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.15
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
21.74kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
59.61kcal/mol
Minimised FF energy
37.87kcal/mol
SASA & burial
✓ computed
SASA (unbound)
699.2Ų
Total solvent-accessible surface area of free ligand
BSA total
474.7Ų
Buried surface area upon binding
BSA apolar
357.3Ų
Hydrophobic contacts buried
BSA polar
117.4Ų
Polar contacts buried
Fraction buried
67.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
75.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2994.2Ų
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
1545.5Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)