Molecular metrics status: done
RDKit SASA-based burial metrics are cached.
SASA cached
3D complex viewer
Viewer legend
Protein receptor
Pocket residues
Cofactor context
Docked ligand
Overall assessment
Reject
SASA cached
Promising but geometrically suspicious
Binding strong
Geometry low
Native strong
SASA done
Strain ΔE
41.3 kcal/mol
Protein clashes
8
Internal clashes
8
Native overlap
contact recall 0.95, Jaccard 0.74, H-bond role recall 0.36
Reason: 8 internal clashes
8 protein-contact clashes
8 intramolecular clashes
61% of hydrophobic surface is solvent-exposed (11/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Molecular report
Reject
Multiple quality flags — this pose should be deprioritised or discarded.
✓ Excellent LE (-1.085 kcal/mol/HA)
✓ Good fit quality (FQ -10.24)
✓ Strong H-bond network (11 bonds)
✓ Deep burial (92% SASA buried)
✓ Lipophilic contacts well-matched (78%)
✗ Extreme strain energy (41.3 kcal/mol)
✗ Geometry warnings
✗ Many internal clashes (13)
Score
-30.367
kcal/mol
LE
-1.085
kcal/mol/HA
Fit Quality
-10.24
FQ (Leeson)
HAC
28
heavy atoms
MW
418
Da
LogP
2.07
cLogP
Interaction summary
HB 11
HY 4
PI 1
CLASH 8
⚠ Exposure 61%
Interaction summary
HB 11
HY 4
PI 1
CLASH 8
⚠ Exposure 61%
Solvent-exposed hydrophobic surface — desolvation penalty likely
61% of hydrophobic surface is solvent-exposed (11/18 atoms). Large non-polar area without protein contacts incurs a desolvation penalty and will reduce binding affinity. Consider truncating or replacing the exposed fragment.
Non-polar atoms 18
Buried (contacted) 7
Exposed 11
LogP 2.07
H-bonds 11
Exposed fragments:
phenyl (6/6 atoms exposed)phenyl (4/6 atoms exposed)aliphatic chain/group (1 atom exposed)
| Final rank | 3.428 | Score | -30.367 |
|---|---|---|---|
| Inter norm | -1.244 | Intra norm | 0.159 |
| Top1000 | no | Excluded | no |
| Contacts | 26 | H-bonds | 11 |
| Artifact reason | geometry warning; 13 clashes; 1 protein clash; high strain Δ 41.3 | ||
| Residues |
ALA158
ALA24
ALA40
ALA70
ASN126
ASN41
ASP129
ASP68
GLN42
GLU43
GLU73
GLY23
GLY25
GLY71
LEU130
LEU39
LYS127
LYS159
LYS26
PHE38
SER157
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 | 20 | Native recall | 0.95 |
| Jaccard | 0.74 | RMSD | - |
| HB strict | 5 | Strict recall | 0.33 |
| 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
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 302 | 0.5239567590025211 | -1.18433 | -30.604 | 9 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 319 | 0.9940520654587742 | -0.944043 | -25.3008 | 5 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 320 | 1.0669444827431311 | -0.878088 | -31.4505 | 3 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 345 | 1.1134646347622539 | -0.877657 | -23.1229 | 3 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 369 | 1.570299553280359 | -0.935163 | -25.1037 | 6 | 14 | 0 | 0.00 | 0.00 | - | no | Open |
| 285 | 1.846962516011115 | -1.10054 | -35.0271 | 11 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 333 | 2.430240854014312 | -0.961348 | -34.1213 | 11 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 313 | 2.7355217655896267 | -0.945999 | -28.0195 | 7 | 18 | 0 | 0.00 | 0.00 | - | no | Open |
| 388 | 3.1357764599548372 | -1.01979 | -35.0482 | 6 | 16 | 0 | 0.00 | 0.00 | - | no | Open |
| 366 | 3.33349022232488 | -1.04252 | -32.8619 | 6 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 313 | 3.427850034969361 | -1.24397 | -30.3675 | 11 | 26 | 20 | 0.95 | 0.36 | - | no | Current |
| 342 | 3.492057571577017 | -0.785111 | -22.7794 | 9 | 15 | 0 | 0.00 | 0.00 | - | no | Open |
| 295 | 3.616137840018539 | -0.981468 | -32.0097 | 7 | 17 | 0 | 0.00 | 0.00 | - | no | Open |
| 437 | 3.855523120955258 | -0.937716 | -27.4849 | 10 | 13 | 0 | 0.00 | 0.00 | - | no | Open |
| 349 | 4.8296015227220686 | -0.681525 | -25.7042 | 8 | 9 | 0 | 0.00 | 0.00 | - | no | Open |
| 361 | 5.231781681702861 | -0.899682 | -33.3801 | 11 | 16 | 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
-30.367kcal/mol
Ligand efficiency (LE)
-1.0846kcal/mol/HA
Score / heavy atom count
Fit quality (FQ)
-10.239
LE / (0.072 + 0.95/HAC) — Leeson & Springthorpe
Heavy atom count
28HA
Physicochemical properties
Molecular weight
417.5Da
Lipinski: ≤ 500 Da
LogP (cLogP)
2.07
Lipinski: ≤ 5
Rotatable bonds
9
Conformational strain (MMFF94s)
Strain energy (ΔE)
41.33kcal/mol
< 5 good · 5–10 marginal · > 10 problematic
Docked FF energy
20.33kcal/mol
Minimised FF energy
-21.00kcal/mol
SASA & burial
✓ computed
SASA (unbound)
661.8Ų
Total solvent-accessible surface area of free ligand
BSA total
609.0Ų
Buried surface area upon binding
BSA apolar
472.5Ų
Hydrophobic contacts buried
BSA polar
136.5Ų
Polar contacts buried
Fraction buried
92.0%
> 60 % indicates good pocket engagement
Lipophilic contact ratio
77.6%
BSA apolar / BSA total — high = hydrophobic driver
Δ Non-polar SASA
-1379.6Ų
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
494.4Ų
Non-polar SASA of full complex (VdW proxy, nonpolar atoms only)