Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
51.6 kcal/mol
Protein clashes
4
Internal clashes
4
Native overlap
contact recall 0.81, Jaccard 0.68, H-bond role recall 0.45
Reason: strain 51.6 kcal/mol
strain ΔE 51.6 kcal/mol
4 protein-contact clashes
4 intramolecular clashes
70% of hydrophobic surface is solvent-exposed (14/20 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
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.152 kcal/mol/HA)
✓ Good fit quality (FQ -11.11)
✓ Strong H-bond network (8 bonds)
✓ Deep burial (89% SASA buried)
✓ Lipophilic contacts well-matched (60%)
✗ Extreme strain energy (51.6 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-34.547
kcal/mol
LE
-1.152
kcal/mol/HA
Fit Quality
-11.11
FQ (Leeson)
HAC
30
heavy atoms
MW
458
Da
LogP
2.66
cLogP
Final rank
3.9958
rank score
Inter norm
-1.223
normalised
Contacts
21
H-bonds 13
Interaction summary
HBD 1
HBA 7
HY 3
PI 1
CLASH 4
Interaction summary
HBD 1
HBA 7
HY 3
PI 1
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
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | 17 | Native recall | 0.81 |
| Jaccard | 0.68 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 258 | 0.25042243857344604 | -1.14891 | -31.0205 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 264 | 1.0927050169268024 | -1.00795 | -24.7925 | 4 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 235 | 1.1073660704846975 | -0.900181 | -23.0605 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 257 | 1.107384658545134 | -0.819468 | -19.7407 | 2 | 17 | 1 | 0.05 | 0.00 | - | no | Open |
| 313 | 1.3452488083914984 | -0.690473 | -17.5537 | 4 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 252 | 1.4292786430260862 | -0.917081 | -25.3234 | 6 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 330 | 1.622607140224942 | -0.920565 | -25.7973 | 2 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 281 | 1.8373311043657956 | -0.808595 | -21.8267 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 206 | 1.8644199550012546 | -0.798056 | -18.2624 | 8 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 361 | 2.311042942916434 | -0.848092 | -25.1719 | 4 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 261 | 2.5727308749693383 | -0.803338 | -20.2039 | 2 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 224 | 2.7169060620044525 | -1.02158 | -27.5832 | 9 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 234 | 3.995775267533372 | -1.22318 | -34.5475 | 13 | 21 | 17 | 0.81 | 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
-34.547kcal/mol
Ligand efficiency (LE)
-1.1516kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-11.109
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
457.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.66
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
51.59kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
108.52kcal/mol
Minimised FF energy
56.93kcal/mol
SASA & burial
✓ computed
SASA (unbound)
696.3Ų
Total solvent-accessible surface area of free ligand
BSA total
619.3Ų
Buried surface area upon binding
BSA apolar
373.6Ų
Hydrophobic contacts buried
BSA polar
245.7Ų
Polar contacts buried
Fraction buried
88.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
60.3%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1313.1Ų
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
501.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)