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
13.3 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 (-1.155 kcal/mol/HA)
✓ Good fit quality (FQ -10.03)
✓ Strong H-bond network (9 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (65%)
✗ Moderate strain (13.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (9)
Score
-25.419
kcal/mol
LE
-1.155
kcal/mol/HA
Fit Quality
-10.03
FQ (Leeson)
HAC
22
heavy atoms
MW
302
Da
LogP
1.99
cLogP
Interaction summary
HB 9
HY 9
PI 0
CLASH 5
⚠ Exposure 40%
Interaction summary
HB 9
HY 9
PI 0
CLASH 5
⚠ Exposure 40%
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
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 1.99
H-bonds 9
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 4.473 | Score | -25.419 |
|---|---|---|---|
| Inter norm | -1.160 | Intra norm | 0.004 |
| Top1000 | no | Excluded | no |
| Contacts | 12 | H-bonds | 9 |
| Artifact reason | geometry warning; 9 clashes; 3 protein clashes | ||
| Residues |
ARG74
ASN208
ASN245
ASP71
GLY214
GLY215
GLY246
LEU73
LYS211
MET70
PRO212
PRO213
| ||
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 | - |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 559 | 0.7198418180090042 | -0.933488 | -20.4818 | 6 | 9 | 0 | 0.00 | - | - | no | Open |
| 525 | 2.4172194168614993 | -1.48041 | -32.0363 | 9 | 18 | 0 | 0.00 | - | - | no | Open |
| 512 | 2.545937422647049 | -1.61802 | -34.0323 | 11 | 17 | 0 | 0.00 | - | - | no | Open |
| 567 | 2.9952729829901434 | -1.24945 | -25.8165 | 9 | 18 | 0 | 0.00 | - | - | no | Open |
| 524 | 3.422947619134114 | -1.36673 | -26.6001 | 13 | 17 | 0 | 0.00 | - | - | no | Open |
| 550 | 3.750956682432338 | -1.21808 | -25.8403 | 6 | 12 | 0 | 0.00 | - | - | no | Open |
| 582 | 4.472569139535506 | -1.15982 | -25.4195 | 9 | 12 | 9 | 0.69 | - | - | no | Current |
| 529 | 4.491059808940537 | -1.52163 | -29.8977 | 11 | 17 | 0 | 0.00 | - | - | no | Open |
| 541 | 5.152210004952779 | -1.44518 | -30.0794 | 11 | 18 | 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
-25.419kcal/mol
Ligand efficiency (LE)
-1.1554kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.031
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
22HA
Physicochemical properties
Molecular weight
302.2Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.99
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
13.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
80.15kcal/mol
Minimised FF energy
66.87kcal/mol
SASA & burial
✓ computed
SASA (unbound)
488.1Ų
Total solvent-accessible surface area of free ligand
BSA total
332.6Ų
Buried surface area upon binding
BSA apolar
215.7Ų
Hydrophobic contacts buried
BSA polar
116.9Ų
Polar contacts buried
Fraction buried
68.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
64.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-2767.2Ų
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
1554.0Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)