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
35.7 kcal/mol
Protein clashes
3
Internal clashes
3
Native overlap
contact recall 0.67, Jaccard 0.54, H-bond role recall 0.45
Reason: no major geometry red flags detected
3 protein-contact clashes
3 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 (-1.267 kcal/mol/HA)
✓ Good fit quality (FQ -10.61)
✓ Strong H-bond network (16 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (66%)
✗ Very high strain energy (35.7 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (5)
Score
-25.346
kcal/mol
LE
-1.267
kcal/mol/HA
Fit Quality
-10.61
FQ (Leeson)
HAC
20
heavy atoms
MW
305
Da
LogP
-2.11
cLogP
Interaction summary
HB 16
HY 2
PI 0
CLASH 3
⚠ Exposure 60%
Interaction summary
HB 16
HY 2
PI 0
CLASH 3
⚠ Exposure 60%
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 -2.11
H-bonds 16
Exposed fragments:
aromatic ring (1/5 atoms exposed)aliphatic chain/group (5 atoms exposed)
| Final rank | 3.764 | Score | -25.346 |
|---|---|---|---|
| Inter norm | -1.532 | Intra norm | 0.264 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 16 |
| Artifact reason | geometry warning; 5 clashes; 3 protein clashes; high strain Δ 34.4 | ||
| Residues |
ALA24
ALA40
ALA70
ASN41
ASP68
GLN42
GLU21
GLU73
GLY23
GLY25
GLY71
LEU39
LYS26
PHE38
SER22
SER27
SER28
THR44
THR69
| ||
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 | ||
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 | 14 | Native recall | 0.67 |
| Jaccard | 0.54 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| HB same residue | 5 | HB residue recall | 0.45 |
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
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 92 | -0.27488169405600155 | -1.23978 | -26.4643 | 11 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 136 | 2.6826692841091115 | -1.97334 | -36.3274 | 16 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 133 | 2.8727048910606037 | -1.53924 | -31.1406 | 7 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 207 | 3.038856002369936 | -1.16176 | -18.4277 | 9 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 117 | 3.1221365776763337 | -1.4511 | -25.135 | 13 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 124 | 3.1723629671495166 | -1.40024 | -20.1365 | 15 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 165 | 3.7635505504674556 | -1.53162 | -25.3456 | 16 | 19 | 14 | 0.67 | 0.45 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-25.346kcal/mol
Ligand efficiency (LE)
-1.2673kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.605
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
20HA
Physicochemical properties
Molecular weight
304.7Da
Lipinski: ≤ 500 Da
LogP (cLogP)
-2.11
Lipinski: ≤ 5
Rotatable bonds
10
Conformational strain (MMFF94s)
Strain energy (ΔE)
35.69kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
110.88kcal/mol
Minimised FF energy
75.19kcal/mol
SASA & burial
✓ computed
SASA (unbound)
479.0Ų
Total solvent-accessible surface area of free ligand
BSA total
441.7Ų
Buried surface area upon binding
BSA apolar
293.4Ų
Hydrophobic contacts buried
BSA polar
148.3Ų
Polar contacts buried
Fraction buried
92.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
66.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1180.7Ų
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
513.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)