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
37.9 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
68% of hydrophobic surface is solvent-exposed (17/25 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 (-0.794 kcal/mol/HA)
✓ Good fit quality (FQ -7.88)
✓ Strong H-bond network (6 bonds)
✓ Deep burial (78% SASA buried)
✓ Lipophilic contacts well-matched (84%)
✗ Very high strain energy (37.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-26.218
kcal/mol
LE
-0.794
kcal/mol/HA
Fit Quality
-7.88
FQ (Leeson)
HAC
33
heavy atoms
MW
471
Da
LogP
1.54
cLogP
Final rank
5.4096
rank score
Inter norm
-0.937
normalised
Contacts
19
H-bonds 8
Interaction summary
HBA 6
HY 2
PI 0
CLASH 3
Interaction summary
HBA 6
HY 2
PI 0
CLASH 3
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: permissive. Residues: 5.
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 | 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 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 106 | 1.0394721556384727 | -0.777083 | -23.5659 | 2 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 98 | 1.2391871940381056 | -0.836962 | -22.2953 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 125 | 1.58867861556985 | -0.808959 | -21.7723 | 4 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 82 | 5.409584212436053 | -0.937495 | -26.2177 | 8 | 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
-26.218kcal/mol
Ligand efficiency (LE)
-0.7945kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-7.883
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
33HA
Physicochemical properties
Molecular weight
470.6Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.54
Lipinski: ≤ 5
Rotatable bonds
7
Conformational strain (MMFF94s)
Strain energy (ΔE)
37.87kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
61.97kcal/mol
Minimised FF energy
24.10kcal/mol
SASA & burial
✓ computed
SASA (unbound)
781.7Ų
Total solvent-accessible surface area of free ligand
BSA total
613.3Ų
Buried surface area upon binding
BSA apolar
512.2Ų
Hydrophobic contacts buried
BSA polar
101.1Ų
Polar contacts buried
Fraction buried
78.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
83.5%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1520.0Ų
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
512.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)