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
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
24.7 kcal/mol
Protein clashes
0
Internal clashes
10
Native overlap
contact recall 0.67, Jaccard 0.54, H-bond role recall 0.36
Reason: 10 internal clashes
10 intramolecular clashes
59% of hydrophobic surface appears solvent-exposed (10/17 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 (-1.219 kcal/mol/HA)
✓ Good fit quality (FQ -10.93)
✓ Strong H-bond network (13 bonds)
✓ Deep burial (87% SASA buried)
✓ Lipophilic contacts well-matched (75%)
✗ High strain energy (24.7 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (10)
Score
-29.258
kcal/mol
LE
-1.219
kcal/mol/HA
Fit Quality
-10.93
FQ (Leeson)
HAC
24
heavy atoms
MW
348
Da
LogP
1.24
cLogP
Interaction summary
HB 13
HY 5
PI 0
CLASH 0
⚠ Exposure 58%
Interaction summary
HB 13
HY 5
PI 0
CLASH 0
⚠ Exposure 58%
Partial hydrophobic solvent exposure
59% of hydrophobic surface appears solvent-exposed (10/17 atoms). Partial exposure is common but may limit selectivity and membrane permeability.
Non-polar atoms 17
Buried (contacted) 7
Exposed 10
LogP 1.24
H-bonds 13
Exposed fragments:
phenyl (6/6 atoms exposed)aliphatic chain/group (4 atoms exposed)
| Final rank | 4.281 | Score | -29.258 |
|---|---|---|---|
| Inter norm | -1.481 | Intra norm | 0.262 |
| Top1000 | no | Excluded | no |
| Contacts | 19 | H-bonds | 13 |
| Artifact reason | geometry warning; 10 clashes; 4 protein clashes; moderate strain Δ 24.7 | ||
| Residues |
ALA24
ALA40
ALA48
ASN41
GLN42
GLU21
GLU73
GLY23
GLY25
GLY47
ILE46
LEU31
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 | 0.54 | 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
No clash · clashes detected for this pose.
All stored poses for this docking hit
| Pose | Final rank | Inter norm | Score | HB | CT | CT overlap | CT recall | HB role rec. | RMSD | Excluded | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 563 | 1.8928814771868634 | -1.35453 | -27.4463 | 5 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 574 | 2.872704971680777 | -0.996415 | -15.7931 | 13 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 592 | 3.431950118215558 | -0.961984 | -15.4549 | 9 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 586 | 4.280581100652397 | -1.48063 | -29.2583 | 13 | 19 | 14 | 0.67 | 0.36 | - | no | Current |
| 570 | 4.765644166236609 | -1.12764 | -20.4843 | 10 | 17 | 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
-29.258kcal/mol
Ligand efficiency (LE)
-1.2191kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.925
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
24HA
Physicochemical properties
Molecular weight
348.4Da
Lipinski: ≤ 500 Da
LogP (cLogP)
1.24
Lipinski: ≤ 5
Rotatable bonds
8
Conformational strain (MMFF94s)
Strain energy (ΔE)
24.68kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
-42.31kcal/mol
Minimised FF energy
-66.99kcal/mol
SASA & burial
✓ computed
SASA (unbound)
597.2Ų
Total solvent-accessible surface area of free ligand
BSA total
520.5Ų
Buried surface area upon binding
BSA apolar
389.4Ų
Hydrophobic contacts buried
BSA polar
131.1Ų
Polar contacts buried
Fraction buried
87.2%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
74.8%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1340.2Ų
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
493.3Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)