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
16.9 kcal/mol
Protein clashes
2
Internal clashes
2
Native overlap
contact recall 0.95, Jaccard 0.87, H-bond role recall 0.64
Reason: no major geometry red flags detected
2 protein-contact clashes
Molecular report
Weak
Marginal quality. Consider only alongside better-scoring alternatives.
✓ Excellent LE (-1.043 kcal/mol/HA)
✓ Good fit quality (FQ -10.06)
✓ Strong H-bond network (12 bonds)
✓ Deep burial (83% SASA buried)
✓ Lipophilic contacts well-matched (77%)
✗ Moderate strain (16.9 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-31.299
kcal/mol
LE
-1.043
kcal/mol/HA
Fit Quality
-10.06
FQ (Leeson)
HAC
30
heavy atoms
MW
398
Da
LogP
3.86
cLogP
Interaction summary
HB 12
HY 8
PI 1
CLASH 2
Interaction summary
HB 12
HY 8
PI 1
CLASH 2
| Final rank | 2.984 | Score | -31.299 |
|---|---|---|---|
| Inter norm | -1.151 | Intra norm | 0.108 |
| Top1000 | no | Excluded | no |
| Contacts | 22 | H-bonds | 12 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash | ||
| Residues |
ALA158
ALA24
ALA40
ASN126
ASN41
ASP129
GLN42
GLU21
GLU43
GLU73
GLY23
GLY25
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
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 | 20 | Native recall | 0.95 |
| Jaccard | 0.87 | RMSD | - |
| HB strict | 8 | Strict recall | 0.53 |
| HB same residue+role | 7 | HB role recall | 0.64 |
| HB same residue | 7 | HB residue recall | 0.64 |
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 419 | 1.3698913484446682 | -1.21986 | -37.7354 | 9 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 474 | 1.8432837421999981 | -0.910572 | -21.9565 | 8 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 383 | 2.5312611190851566 | -0.94378 | -32.6909 | 6 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 416 | 2.9837563668447795 | -1.15112 | -31.2989 | 12 | 22 | 20 | 0.95 | 0.64 | - | no | Current |
| 446 | 3.147913771556294 | -1.07455 | -32.5822 | 7 | 12 | 0 | 0.00 | 0.00 | - | no | Open |
| 443 | 3.27891113853971 | -0.71915 | -21.2671 | 8 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 397 | 4.450463944905651 | -0.904324 | -25.6236 | 8 | 20 | 0 | 0.00 | 0.00 | - | no | Open |
| 405 | 4.779173564879599 | -0.794952 | -21.6784 | 7 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 425 | 5.063047121982455 | -0.974088 | -31.2835 | 7 | 12 | 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
-31.299kcal/mol
Ligand efficiency (LE)
-1.0433kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.064
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
30HA
Physicochemical properties
Molecular weight
398.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
3.86
Lipinski: ≤ 5
Rotatable bonds
5
Conformational strain (MMFF94s)
Strain energy (ΔE)
16.88kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
115.41kcal/mol
Minimised FF energy
98.54kcal/mol
SASA & burial
✓ computed
SASA (unbound)
670.0Ų
Total solvent-accessible surface area of free ligand
BSA total
555.8Ų
Buried surface area upon binding
BSA apolar
427.2Ų
Hydrophobic contacts buried
BSA polar
128.6Ų
Polar contacts buried
Fraction buried
82.9%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
76.9%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1377.0Ų
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
529.6Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)