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
32.3 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.90, Jaccard 0.70, H-bond role recall 0.18
Reason: no major geometry red flags detected
1 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.099 kcal/mol/HA)
✓ Good fit quality (FQ -9.99)
✓ Good H-bonds (5 bonds)
✓ Deep burial (93% SASA buried)
✓ Lipophilic contacts well-matched (94%)
✗ Very high strain energy (32.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (11)
Score
-27.464
kcal/mol
LE
-1.099
kcal/mol/HA
Fit Quality
-9.99
FQ (Leeson)
HAC
25
heavy atoms
MW
332
Da
LogP
3.04
cLogP
Final rank
2.1158
rank score
Inter norm
-1.320
normalised
Contacts
25
H-bonds 6
Interaction summary
HBD 3
HBA 2
HY 2
PI 1
CLASH 1
Interaction summary
HBD 3
HBA 2
HY 2
PI 1
CLASH 1
HBD/HBA · H-bonds (geometric)
HBD = ligand donates H · HBA = ligand accepts H · ~ = weak (≥110°). Mode: strict. Residues: 4.
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: 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 | 19 | Native recall | 0.90 |
| Jaccard | 0.70 | RMSD | - |
| HB strict | 2 | Strict recall | 0.13 |
| HB same residue+role | 2 | HB role recall | 0.18 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 57 | 0.9427582994708326 | -0.998639 | -22.6939 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 33 | 2.115820565657674 | -1.31981 | -27.4636 | 6 | 25 | 19 | 0.90 | 0.18 | - | no | Current |
| 51 | 2.453987996494834 | -0.978162 | -20.5051 | 5 | 16 | 1 | 0.05 | 0.00 | - | no | Open |
| 61 | 4.81138704349993 | -1.01896 | -24.178 | 6 | 18 | 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
-27.464kcal/mol
Ligand efficiency (LE)
-1.0985kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.987
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
25HA
Physicochemical properties
Molecular weight
332.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.04
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
32.27kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
103.34kcal/mol
Minimised FF energy
71.07kcal/mol
SASA & burial
✓ computed
SASA (unbound)
615.8Ų
Total solvent-accessible surface area of free ligand
BSA total
572.3Ų
Buried surface area upon binding
BSA apolar
537.9Ų
Hydrophobic contacts buried
BSA polar
34.4Ų
Polar contacts buried
Fraction buried
92.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
94.0%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1436.1Ų
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
506.2Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)