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 mixed
SASA done
Strain ΔE
31.7 kcal/mol
Protein clashes
5
Internal clashes
5
Native overlap
contact recall 0.48, Jaccard 0.32, H-bond role recall 0.27
Reason: no major geometry red flags detected
5 protein-contact clashes
5 intramolecular clashes
60% of hydrophobic surface is solvent-exposed (6/10 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.540 kcal/mol/HA)
✓ Good fit quality (FQ -12.63)
✓ Strong H-bond network (16 bonds)
✓ Deep burial (88% SASA buried)
✓ Lipophilic contacts well-matched (69%)
✗ Very high strain energy (31.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-29.268
kcal/mol
LE
-1.540
kcal/mol/HA
Fit Quality
-12.63
FQ (Leeson)
HAC
19
heavy atoms
MW
281
Da
LogP
-0.26
cLogP
Interaction summary
HB 16
HY 1
PI 0
CLASH 5
⚠ Exposure 60%
Interaction summary
HB 16
HY 1
PI 0
CLASH 5
⚠ Exposure 60%
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
Solvent-exposed hydrophobic surface — desolvation penalty likely
60% of hydrophobic surface is solvent-exposed (6/10 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 10
Buried (contacted) 4
Exposed 6
LogP -0.26
H-bonds 16
Exposed fragments:
phenyl (6/6 atoms exposed)
| Final rank | 2.682 | Score | -29.268 |
|---|---|---|---|
| Inter norm | -1.695 | Intra norm | 0.154 |
| Top1000 | no | Excluded | no |
| Contacts | 20 | H-bonds | 16 |
| Artifact reason | geometry warning; 8 clashes; 1 protein clash; high strain Δ 31.7 | ||
| Residues |
ALA24
ALA48
ALA49
ALA70
ASP68
GLN42
GLU21
GLU43
GLU73
GLY23
GLY25
GLY47
GLY71
ILE46
LYS26
SER22
SER27
SER28
THR44
THR69
| ||
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: strict.
| Name | RAB5A | Contacts | 21 |
|---|---|---|---|
| Pose | Open native pose | HB | 0 |
| IFP residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU73
GLY23
GLY25
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
SER22
SER27
SER28
| ||
| Current overlap | 10 | Native recall | 0.48 |
| Jaccard | 0.32 | RMSD | - |
| HB strict | 4 | Strict recall | 0.27 |
| HB same residue+role | 3 | HB role recall | 0.27 |
| HB same residue | 3 | HB residue recall | 0.27 |
Protein summary
165 residues
| Protein target | T22 | Atoms | 2561 |
|---|---|---|---|
| Residues | 165 | Chains | 1 |
| Residue summary | LEU:363; LYS:242; ALA:231; ARG:214; ILE:190; GLU:180; VAL:144; SER:143; PHE:140; ASN:112; THR:112; TYR:105; GLN:102; ASP:96; GLY:77; TRP:48 | ||
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 305 | 1.0227578376082587 | -1.63221 | -29.0736 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 339 | 1.0977752334667914 | -1.50379 | -27.2444 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 364 | 1.3242847920907537 | -1.42014 | -26.0848 | 7 | 10 | 0 | 0.00 | 0.00 | - | no | Open |
| 318 | 1.677371121731007 | -1.19289 | -20.0023 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 404 | 2.029490729260137 | -1.22908 | -23.3088 | 8 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 305 | 2.6817761148920427 | -1.69453 | -29.2684 | 16 | 20 | 10 | 0.48 | 0.27 | - | no | Current |
| 264 | 4.247124566588215 | -1.25775 | -22.5757 | 14 | 11 | 0 | 0.00 | 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
-29.268kcal/mol
Ligand efficiency (LE)
-1.5404kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.627
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
19HA
Physicochemical properties
Molecular weight
281.3Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-0.26
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
31.67kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-132.97kcal/mol
Minimised FF energy
-164.65kcal/mol
SASA & burial
✓ computed
SASA (unbound)
475.1Ų
Total solvent-accessible surface area of free ligand
BSA total
420.2Ų
Buried surface area upon binding
BSA apolar
290.4Ų
Hydrophobic contacts buried
BSA polar
129.8Ų
Polar contacts buried
Fraction buried
88.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
69.1%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1206.3Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
507.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)