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
36.4 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.67, Jaccard 0.61, H-bond role recall 0.36
Reason: no major geometry red flags detected
2 protein-contact clashes
58% of hydrophobic surface appears solvent-exposed (11/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.032 kcal/mol/HA)
✓ Good fit quality (FQ -9.74)
✓ Strong H-bond network (10 bonds)
✓ Deep burial (68% SASA buried)
✓ Lipophilic contacts well-matched (74%)
✗ Very high strain energy (36.4 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (12)
Score
-28.890
kcal/mol
LE
-1.032
kcal/mol/HA
Fit Quality
-9.74
FQ (Leeson)
HAC
28
heavy atoms
MW
400
Da
LogP
1.13
cLogP
Interaction summary
HB 10
HY 1
PI 0
CLASH 2
⚠ Exposure 57%
Interaction summary
HB 10
HY 1
PI 0
CLASH 2
⚠ Exposure 57%
Partial hydrophobic solvent exposure
58% of hydrophobic surface appears solvent-exposed (11/19 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 19
Buried (contacted) 8
Exposed 11
LogP 1.13
H-bonds 10
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (5/6 atoms exposed)
| Final rank | 4.728 | Score | -28.890 |
|---|---|---|---|
| Inter norm | -1.164 | Intra norm | 0.132 |
| Top1000 | no | Excluded | no |
| Contacts | 16 | H-bonds | 10 |
| Artifact reason | geometry warning; 12 clashes; 3 protein clashes; high strain Δ 36.4 | ||
| Residues |
ALA24
ALA40
ASN41
GLN42
GLU21
GLU43
GLU73
GLY23
GLY25
LEU39
LYS26
PHE38
SER22
SER27
SER28
THR44
| ||
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 | 0.61 | RMSD | - |
| HB strict | 6 | Strict recall | 0.40 |
| HB same residue+role | 4 | HB role recall | 0.36 |
| 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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 77 | 2.876430342267816 | -0.922413 | -22.2431 | 5 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 114 | 2.883794498530214 | -1.02014 | -26.3795 | 3 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 101 | 2.9293523248686655 | -0.843323 | -23.4699 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 114 | 3.601961305920066 | -1.19695 | -28.055 | 4 | 21 | 0 | 0.00 | 0.00 | - | no | Open |
| 85 | 3.6319795394564807 | -0.83297 | -17.4434 | 6 | 19 | 0 | 0.00 | 0.00 | - | no | Open |
| 71 | 4.15022742952253 | -1.05998 | -23.809 | 15 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 71 | 4.421576432535559 | -0.829435 | -18.9188 | 4 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 89 | 4.489621695148427 | -0.89201 | -19.623 | 10 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 92 | 4.6462206342733205 | -0.843229 | -22.0498 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 64 | 4.727763877486028 | -1.16427 | -28.89 | 10 | 16 | 14 | 0.67 | 0.36 | - | no | Current |
| 44 | 6.009884957343629 | -1.02072 | -18.2378 | 15 | 15 | 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
-28.890kcal/mol
Ligand efficiency (LE)
-1.0318kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-9.740
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
400.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.13
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
36.35kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-90.88kcal/mol
Minimised FF energy
-127.24kcal/mol
SASA & burial
✓ computed
SASA (unbound)
674.5Ų
Total solvent-accessible surface area of free ligand
BSA total
462.0Ų
Buried surface area upon binding
BSA apolar
343.5Ų
Hydrophobic contacts buried
BSA polar
118.5Ų
Polar contacts buried
Fraction buried
68.5%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.4%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1383.9Ų
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
532.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)