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 high
Native strong
SASA done
Strain ΔE
22.8 kcal/mol
Protein clashes
1
Internal clashes
1
Native overlap
contact recall 0.76, Jaccard 0.70, H-bond role recall 0.45
Reason: no major geometry red flags detected
1 protein-contact clashes
54% of hydrophobic surface appears solvent-exposed (7/13 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 (-1.514 kcal/mol/HA)
✓ Good fit quality (FQ -12.91)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (70%)
✗ High strain energy (22.8 kcal/mol)
✗ Geometry warnings
✗ Internal clashes (8)
Score
-31.788
kcal/mol
LE
-1.514
kcal/mol/HA
Fit Quality
-12.91
FQ (Leeson)
HAC
21
heavy atoms
MW
326
Da
LogP
0.81
cLogP
Interaction summary
HB 11
HY 5
PI 1
CLASH 1
⚠ Exposure 53%
Interaction summary
HB 11
HY 5
PI 1
CLASH 1
⚠ Exposure 53%
Partial hydrophobic solvent exposure
54% of hydrophobic surface appears solvent-exposed (7/13 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 13
Buried (contacted) 6
Exposed 7
LogP 0.81
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.592 | Score | -31.788 |
|---|---|---|---|
| Inter norm | -1.540 | Intra norm | 0.026 |
| Top1000 | no | Excluded | no |
| Contacts | 18 | H-bonds | 11 |
| Artifact reason | geometry warning; 8 clashes; 3 protein clashes; moderate strain Δ 22.8 | ||
| Residues |
ALA158
ALA24
ASN126
ASN41
GLN42
GLU21
GLU73
GLY23
GLY25
LYS127
LYS159
LYS26
PHE38
SER22
SER27
SER28
THR44
THR69
| ||
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 | 16 | Native recall | 0.76 |
| Jaccard | 0.70 | RMSD | - |
| HB strict | 7 | Strict recall | 0.47 |
| HB same residue+role | 5 | HB role recall | 0.45 |
| 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
Native π–π recall is disabled because no explicit native π–π reference was stored.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 508 | 2.009788458540564 | -1.01822 | -20.5996 | 7 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 545 | 3.4732770804134097 | -1.18527 | -23.981 | 4 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 466 | 3.510541205591343 | -1.43344 | -28.2186 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 482 | 3.5921666043258553 | -1.53996 | -31.7883 | 11 | 18 | 16 | 0.76 | 0.45 | - | no | Current |
| 469 | 3.966350797122376 | -1.20182 | -23.6843 | 13 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 474 | 4.003880070761457 | -1.66085 | -33.326 | 9 | 23 | 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
-31.788kcal/mol
Ligand efficiency (LE)
-1.5137kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-12.912
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
21HA
Physicochemical properties
Molecular weight
326.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
0.81
Lipinski: ≤ 5
Rotatable bonds
6
Conformational strain (MMFF94s)
Strain energy (ΔE)
22.81kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-148.68kcal/mol
Minimised FF energy
-171.49kcal/mol
SASA & burial
✓ computed
SASA (unbound)
513.7Ų
Total solvent-accessible surface area of free ligand
BSA total
445.5Ų
Buried surface area upon binding
BSA apolar
312.8Ų
Hydrophobic contacts buried
BSA polar
132.7Ų
Polar contacts buried
Fraction buried
86.7%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
70.2%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1220.1Ų
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
499.9Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)