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
24.3 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.52, Jaccard 0.35, H-bond role recall 0.36
Reason: no major geometry red flags detected
4 protein-contact clashes
4 intramolecular clashes
65% of hydrophobic surface is solvent-exposed (11/17 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 (-1.126 kcal/mol/HA)
✓ Good fit quality (FQ -10.38)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ High strain energy (24.3 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-29.278
kcal/mol
LE
-1.126
kcal/mol/HA
Fit Quality
-10.38
FQ (Leeson)
HAC
26
heavy atoms
MW
377
Da
LogP
0.95
cLogP
Final rank
5.0165
rank score
Inter norm
-1.229
normalised
Contacts
21
H-bonds 16
Interaction summary
HBD 3
HBA 5
HY 3
PI 0
CLASH 4
Interaction summary
HBD 3
HBA 5
HY 3
PI 0
CLASH 4
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 6.
PI · π–π interactions
No pi · π–π interactions detected for this pose.
HY · Hydrophobic contacts
CLASH · Clashes
Native ligand reference
★ reference
Interaction fingerprint calculated directly from the uploaded native ligand without docking. Current H-bond mode: permissive.
| 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 | 11 | Native recall | 0.52 |
| Jaccard | 0.35 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| HB same residue | 4 | HB residue recall | 0.36 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 63 | 1.992548884312731 | -1.30848 | -32.1669 | 13 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 98 | 3.3548680929980264 | -1.08604 | -27.0791 | 7 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 66 | 3.7209418269626306 | -0.960993 | -21.8361 | 15 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 54 | 4.05191409116451 | -1.20808 | -28.3426 | 12 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 100 | 4.364750326690326 | -0.79464 | -19.9392 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 52 | 5.016463742920565 | -1.22923 | -29.2776 | 16 | 21 | 11 | 0.52 | 0.36 | - | no | Current |
Molecular metrics
RDKit SASA burial, strain energy (MMFF94s), ligand efficiency and fit quality for this docking pose.
Scoring & efficiency
Docking score
-29.278kcal/mol
Ligand efficiency (LE)
-1.1261kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.375
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
26HA
Physicochemical properties
Molecular weight
376.8Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.95
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.28kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
82.14kcal/mol
Minimised FF energy
57.86kcal/mol
SASA & burial
✓ computed
SASA (unbound)
576.1Ų
Total solvent-accessible surface area of free ligand
BSA total
514.6Ų
Buried surface area upon binding
BSA apolar
398.1Ų
Hydrophobic contacts buried
BSA polar
116.4Ų
Polar contacts buried
Fraction buried
89.3%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1299.4Ų
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
1368.5Ų
Non-polar SASA of receptor alone (VdW proxy, nonpolar atoms only)
Complex non-polar SASA
519.7Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)